rs6477258

Variant names:

• chr9-8095638-T-C
• rs6477258

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 0.714 in 150,612 control chromosomes in the GnomAD database, including 38,553 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 0.71 (38553 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 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: 0.714 AC: 107387 AN: 150494 Hom.: 38519 Cov.: 25

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.714 AC: 107477 AN: 150612 Hom.: 38553 Cov.: 25 AF XY: 0.717 AC XY: 52703 AN XY: 73482

African (AFR) AF: 0.711 AC: 29223 AN: 41100

American (AMR) AF: 0.709 AC: 10663 AN: 15032

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1897 AN: 3448

East Asian (EAS) AF: 0.658 AC: 3346 AN: 5086

South Asian (SAS) AF: 0.670 AC: 3164 AN: 4722

European-Finnish (FIN) AF: 0.805 AC: 8299 AN: 10312

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48703 AN: 67642

Other (OTH) AF: 0.672 AC: 1394 AN: 2074

Alfa AF: 0.710 Hom.: 48608

Bravo AF: 0.706

Asia WGS AF: 0.663 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs6477258; hg19: chr9-8095638; COSMIC: COSV69445834;