rs4837960

Variant names:

• chr9-122361692-G-T
• rs4837960

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 0.204 in 152,084 control chromosomes in the GnomAD database, including 4,010 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 0.20 (4010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.204 AC: 30957 AN: 151966 Hom.: 4003 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.204 AC: 31012 AN: 152084 Hom.: 4010 Cov.: 32 AF XY: 0.203 AC XY: 15067 AN XY: 74336

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.174

Alfa AF: 0.148 Hom.: 2542

Bravo AF: 0.201

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837960; hg19: chr9-125123971;