rs7025295

Variant names:

• chr9-6395247-T-C
• rs7025295

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 0.335 in 152,114 control chromosomes in the GnomAD database, including 8,982 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 0.34 (8982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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: 0.336 AC: 50995 AN: 151996 Hom.: 8980 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.335 AC: 51009 AN: 152114 Hom.: 8982 Cov.: 32 AF XY: 0.340 AC XY: 25303 AN XY: 74350

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.359

Alfa AF: 0.372 Hom.: 18464

Bravo AF: 0.326

Asia WGS AF: 0.265 AC: 921 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7025295; hg19: chr9-6395247;