rs3117604

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.470

Alfa AF: 0.339 Hom.: 9559

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117604; hg19: chr4-74734668;