rs4837656

Variant names:

• chr9-119671775-T-C
• rs4837656

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 0.267 in 151,946 control chromosomes in the GnomAD database, including 5,798 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 0.27 (5798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.267 AC: 40553 AN: 151828 Hom.: 5785 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.267 AC: 40612 AN: 151946 Hom.: 5798 Cov.: 32 AF XY: 0.266 AC XY: 19759 AN XY: 74260

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0248

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.258

Alfa AF: 0.285 Hom.: 12961

Bravo AF: 0.256

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837656; hg19: chr9-122434053; COSMIC: COSV60399620;