rs477515

Variant names:

• chr6-32601914-G-A
• rs477515

Your query was ambiguous. Multiple possible variants found:

• chr6-32601914-G-A
• chr6-32601914-G-C
• chr6-32601914-G-T

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 0.27 in 151,464 control chromosomes in the GnomAD database, including 5,880 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 0.27 (5880 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 130 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.32 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: 0.270 AC: 40824 AN: 151342 Hom.: 5879 Cov.: 29

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.270 AC: 40851 AN: 151464 Hom.: 5880 Cov.: 29 AF XY: 0.264 AC XY: 19563 AN XY: 73988

African (AFR) AF: 0.216 AC: 8925 AN: 41328

American (AMR) AF: 0.328 AC: 4989 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1150 AN: 3466

East Asian (EAS) AF: 0.194 AC: 998 AN: 5138

South Asian (SAS) AF: 0.246 AC: 1178 AN: 4790

European-Finnish (FIN) AF: 0.196 AC: 2057 AN: 10470

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20513 AN: 67758

Other (OTH) AF: 0.278 AC: 586 AN: 2106

Alfa AF: 0.299 Hom.: 21015

Bravo AF: 0.286

Asia WGS AF: 0.210 AC: 732 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs477515; hg19: chr6-32569691;