dbSNP rs11628587: ENSG00000254718:n.2267G>A (chr14-60240713-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000532515.1(ENSG00000254718):n.2267G>A 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 0.346 in 152,054 control chromosomes in the GnomAD database, including 9,878 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 0.35 ( 9878 hom., cov: 33)

Exomes 𝑓: 0.30 ( 0 hom. )

Consequence

ENSG00000254718
ENST00000532515.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.440

Publications

3 publications found

Variant links:

Genes affected

ENSG00000254718 (HGNC:):

ENSG00000254718 links:

Genome browser will be placed here

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=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927702	NR_188027.1 link	n.201-259G>A		intron_variant	Intron 2 of 2
LOC101927702	NR_188028.1 link	n.280-259G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000254718	ENST00000532515.1 link	n.2267G>A	non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000254718	ENST00000529171.5 link	n.235-259G>A	intron_variant	Intron 2 of 2	3
ENSG00000254718	ENST00000553269.6 link	n.283-259G>A	intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52486

AN:

151924

Hom.:

9861

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.325

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

Cov.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.346

AC:

52544

AN:

152044

Hom.:

9878

Cov.:

AF XY:

0.341

AC XY:

25326

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.500

AC:

20751

AN:

41464

American (AMR)

AF:

0.266

AC:

4070

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.403

AC:

1400

AN:

3470

East Asian (EAS)

AF:

0.129

AC:

666

AN:

5170

South Asian (SAS)

AF:

0.439

AC:

2116

AN:

4824

European-Finnish (FIN)

AF:

0.261

AC:

2756

AN:

10568

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19912

AN:

67946

Other (OTH)

AF:

0.321

AC:

679

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1744

3488

5231

6975

8719

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.315

Hom.:

1470

Bravo

AF:

0.350

Asia WGS

AF:

0.275

AC:

959

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.9

(source)

DANN

Benign

0.80

PhyloP100

0.44

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over