Genetic Variant ENSG00000274310:n.196-480T>G (chr8-54469706-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000610741.1(ENSG00000274310):n.196-480T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,226 control chromosomes in the GnomAD database, including 2,127 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 0.15 ( 2127 hom., cov: 33)

Consequence

ENSG00000274310
ENST00000610741.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.113

Publications

2 publications found

Variant links:

Genes affected

ENSG00000274310 (HGNC:):

ENSG00000274310 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 (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100129098	XM_041680557.1 link	c.454+267A>C		intron_variant	Intron 1 of 1		XP_041536491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000274310	ENST00000610741.1 link	n.196-480T>G		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22974

AN:

152108

Hom.:

2122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0443

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.151

AC:

22982

AN:

152226

Hom.:

2127

Cov.:

AF XY:

0.150

AC XY:

11181

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0442

AC:

1838

AN:

41560

American (AMR)

AF:

0.159

AC:

2440

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

887

AN:

3464

East Asian (EAS)

AF:

0.278

AC:

1436

AN:

5160

South Asian (SAS)

AF:

0.138

AC:

665

AN:

4822

European-Finnish (FIN)

AF:

0.163

AC:

1726

AN:

10606

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.197

AC:

13377

AN:

67988

Other (OTH)

AF:

0.184

AC:

389

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1002

2004

3005

4007

5009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.144

Hom.:

266

Bravo

AF:

0.146

Asia WGS

AF:

0.197

AC:

683

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

2.2

(source)

DANN

Benign

0.66

PhyloP100

0.11

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