rs1017643

Variant names:

• chr6-156472999-G-A
• rs1017643

Your query was ambiguous. Multiple possible variants found:

• chr6-156472999-G-A
• chr6-156472999-G-C

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 0.5 in 151,996 control chromosomes in the GnomAD database, including 23,190 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 0.50 (23190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 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: 0.500 AC: 75949 AN: 151878 Hom.: 23188 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.500 AC: 75943 AN: 151996 Hom.: 23190 Cov.: 32 AF XY: 0.497 AC XY: 36916 AN XY: 74292

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.547

Alfa AF: 0.643 Hom.: 27172

Bravo AF: 0.481

Asia WGS AF: 0.386 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017643; hg19: chr6-156794133;