dbSNP rs7534271: ENSG00000226252:n.1595C>G (chr1-47228309-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000422216.1(ENSG00000226252):n.1595C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 177,046 control chromosomes in the GnomAD database, including 22,915 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 19614 hom., cov: 32)

Exomes 𝑓: 0.45 ( 3301 hom. )

Consequence

ENSG00000226252
ENST00000422216.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.555

Publications

5 publications found

Variant links:

Genes affected

ENSG00000226252 (HGNC:):

ENSG00000226252 links:

TAL1 (HGNC:11556): (TAL bHLH transcription factor 1, erythroid differentiation factor) Enables several functions, including DNA-binding transcription factor activity; E-box binding activity; and histone deacetylase binding activity. Involved in several processes, including myeloid cell differentiation; positive regulation of cellular component organization; and positive regulation of erythrocyte differentiation. Located in chromatin and nucleoplasm. Part of transcription regulator complex. Implicated in acute lymphoblastic leukemia. [provided by Alliance of Genome Resources, Apr 2022]

TAL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAL1	NM_001290403.2 link	c.-2+887G>C		intron_variant	Intron 2 of 4	ENST00000691006.1	NP_001277332.1	P17542-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAL1	ENST00000691006.1 link	c.-2+887G>C		intron_variant	Intron 2 of 4		NM_001290403.2	ENSP00000510655.1		P17542-1

Frequencies

GnomAD3 genomes

AF:

0.480

AC:

72981

AN:

151906

Hom.:

19593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.637

Gnomad EAS

AF:

0.0174

Gnomad SAS

AF:

0.464

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.502

GnomAD4 exome

AF:

0.449

AC:

11233

AN:

25020

Hom.:

3301

Cov.:

AF XY:

0.453

AC XY:

5186

AN XY:

11446

show subpopulations

African (AFR)

AF:

0.309

AC:

249

AN:

806

American (AMR)

AF:

0.467

AC:

252

AN:

540

Ashkenazi Jewish (ASJ)

AF:

0.647

AC:

1028

AN:

1588

East Asian (EAS)

AF:

0.00241

AC:

AN:

5394

South Asian (SAS)

AF:

0.388

AC:

AN:

214

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.671

AC:

102

AN:

152

European-Non Finnish (NFE)

AF:

0.594

AC:

8495

AN:

14312

Other (OTH)

AF:

0.503

AC:

1008

AN:

2002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

203

407

610

814

1017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.480

AC:

73036

AN:

152026

Hom.:

19614

Cov.:

AF XY:

0.478

AC XY:

35484

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.299

AC:

12401

AN:

41476

American (AMR)

AF:

0.441

AC:

6731

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.637

AC:

2210

AN:

3468

East Asian (EAS)

AF:

0.0176

AC:

AN:

5174

South Asian (SAS)

AF:

0.466

AC:

2244

AN:

4814

European-Finnish (FIN)

AF:

0.632

AC:

6664

AN:

10544

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.603

AC:

40988

AN:

67972

Other (OTH)

AF:

0.504

AC:

1064

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1745

3489

5234

6978

8723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.551

Hom.:

3009

Bravo

AF:

0.455

Asia WGS

AF:

0.270

AC:

942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.8

(source)

DANN

Benign

0.46

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs7534271

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over