rs3117604

Variant names:

• chr4-73868951-T-C
• rs3117604

Your query was ambiguous. Multiple possible variants found:

• chr4-73868951-T-C
• chr4-73868951-T-G

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 0.468 in 151,674 control chromosomes in the GnomAD database, including 20,092 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 0.47 (20092 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.467 AC: 70803 AN: 151552 Hom.: 20030 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.468 AC: 70925 AN: 151674 Hom.: 20092 Cov.: 31 AF XY: 0.466 AC XY: 34578 AN XY: 74140

African (AFR) AF: 0.795 AC: 32989 AN: 41474

American (AMR) AF: 0.503 AC: 7680 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3464

East Asian (EAS) AF: 0.457 AC: 2327 AN: 5094

South Asian (SAS) AF: 0.378 AC: 1811 AN: 4796

European-Finnish (FIN) AF: 0.291 AC: 3071 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20228 AN: 67720

Other (OTH) AF: 0.470 AC: 992 AN: 2112

Alfa AF: 0.360 Hom.: 14495

Bravo AF: 0.499

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-1.3
PromoterAI		0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3117604; hg19: chr4-74734668;