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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.278

Alfa AF: 0.297 Hom.: 6939

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs477515; hg19: chr6-32569691;