rs4977974

Positions:

• chr9-25294703-T-C

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/exons	MANE	UniProt

Ensembl

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