rs7865955

Variant names:

• chr9-6408247-G-C
• rs7865955

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 0.513 in 152,076 control chromosomes in the GnomAD database, including 21,000 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 0.51 (21000 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.513 AC: 77946 AN: 151958 Hom.: 20984 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.513 AC: 77978 AN: 152076 Hom.: 21000 Cov.: 33 AF XY: 0.514 AC XY: 38189 AN XY: 74344

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.513

Alfa AF: 0.545 Hom.: 2938

Bravo AF: 0.504

Asia WGS AF: 0.699 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7865955; hg19: chr9-6408247; COSMIC: COSV71883187;