chr4-124778759-A-C

Variant names:

• chr4-124778759-A-C
• rs7661684

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 0.359 in 151,374 control chromosomes in the GnomAD database, including 9,997 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 0.36 (9997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 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: 0.359 AC: 54265 AN: 151256 Hom.: 9981 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.359 AC: 54316 AN: 151374 Hom.: 9997 Cov.: 31 AF XY: 0.365 AC XY: 27026 AN XY: 73966

African (AFR) AF: 0.327 AC: 13532 AN: 41324

American (AMR) AF: 0.369 AC: 5616 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3464

East Asian (EAS) AF: 0.641 AC: 3303 AN: 5156

South Asian (SAS) AF: 0.467 AC: 2239 AN: 4798

European-Finnish (FIN) AF: 0.410 AC: 4213 AN: 10274

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22811 AN: 67836

Other (OTH) AF: 0.360 AC: 757 AN: 2102

Alfa AF: 0.344 Hom.: 4812

Bravo AF: 0.352

Asia WGS AF: 0.536 AC: 1858 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7661684; hg19: chr4-125699914;