rs4977950

chr9-24732484-G-Cchr9-24732484-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 0.201 in 151,858 control chromosomes in the GnomAD database, including 4,327 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 (4327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.201 AC: 30516 AN: 151740 Hom.: 4316 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.201 AC: 30536 AN: 151858 Hom.: 4327 Cov.: 32 AF XY: 0.213 AC XY: 15778 AN XY: 74206

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.186

Alfa AF: 0.157 Hom.: 282

Bravo AF: 0.209

Asia WGS AF: 0.468 AC: 1617 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4977950; hg19: chr9-24732482;