4-73872737-C-G

Variant names:

• chr4-73872737-C-G
• rs3097411

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 0.419 in 151,798 control chromosomes in the GnomAD database, including 16,849 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 0.42 (16849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 3 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 = 0.739 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: 0.418 AC: 63440 AN: 151680 Hom.: 16787 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.419 AC: 63560 AN: 151798 Hom.: 16849 Cov.: 32 AF XY: 0.419 AC XY: 31072 AN XY: 74174

African (AFR) AF: 0.746 AC: 30826 AN: 41308

American (AMR) AF: 0.457 AC: 6962 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3464

East Asian (EAS) AF: 0.434 AC: 2233 AN: 5144

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4818

European-Finnish (FIN) AF: 0.259 AC: 2731 AN: 10562

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16461 AN: 67944

Other (OTH) AF: 0.423 AC: 893 AN: 2110

Alfa AF: 0.322 Hom.: 1268

Bravo AF: 0.451

Asia WGS AF: 0.426 AC: 1480 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	0.16
DANN	Benign	0.44
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs3097411; hg19: chr4-74738454; COSMIC: COSV67611914;