rs4837960

chr9-122361692-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;