4-122699757-T-G

Variant names:

• chr4-122699757-T-G
• rs309414

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.658 in 152,122 control chromosomes in the GnomAD database, including 34,024 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 0.66 (34024 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99999 AN: 152004 Hom.: 33996 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.658 AC: 100080 AN: 152122 Hom.: 34024 Cov.: 33 AF XY: 0.655 AC XY: 48724 AN XY: 74360

African (AFR) AF: 0.734 AC: 30463 AN: 41484

American (AMR) AF: 0.721 AC: 11011 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.954 AC: 4932 AN: 5172

South Asian (SAS) AF: 0.869 AC: 4192 AN: 4826

European-Finnish (FIN) AF: 0.408 AC: 4316 AN: 10572

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40303 AN: 68002

Other (OTH) AF: 0.660 AC: 1392 AN: 2108

Alfa AF: 0.621 Hom.: 115662

Bravo AF: 0.685

Asia WGS AF: 0.880 AC: 3058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs309414; hg19: chr4-123620912;