rs4977974

Variant names:

• chr9-25294703-T-C
• rs4977974

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 0.349 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.349 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

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.293

Alfa AF: 0.257 Hom.: 7936

Bravo AF: 0.366

Asia WGS AF: 0.298 AC: 1030 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
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: rs4977974; hg19: chr9-25294701;