rs4977974

Variant names:

• chr9-25294703-T-C
• rs4977974

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 0.349 in 151,926 control chromosomes in the GnomAD database, including 10,742 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 0.35 (10742 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52996 AN: 151808 Hom.: 10707 Cov.: 33

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.349 AC: 53085 AN: 151926 Hom.: 10742 Cov.: 33 AF XY: 0.350 AC XY: 26002 AN XY: 74266

African (AFR) AF: 0.553 AC: 22930 AN: 41446

American (AMR) AF: 0.377 AC: 5737 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1273 AN: 5164

South Asian (SAS) AF: 0.277 AC: 1339 AN: 4828

European-Finnish (FIN) AF: 0.322 AC: 3395 AN: 10554

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16925 AN: 67928

Other (OTH) AF: 0.293 AC: 617 AN: 2108

Alfa AF: 0.261 Hom.: 10766

Bravo AF: 0.366

Asia WGS AF: 0.298 AC: 1030 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.56
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4977974; hg19: chr9-25294701;