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. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.138 AC: 5702 AN: 41438

American (AMR) AF: 0.569 AC: 8696 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1933 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1919 AN: 5162

South Asian (SAS) AF: 0.474 AC: 2278 AN: 4808

European-Finnish (FIN) AF: 0.666 AC: 7036 AN: 10560

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.684 AC: 46509 AN: 67980

Other (OTH) AF: 0.547 AC: 1150 AN: 2104

Alfa AF: 0.636 Hom.: 32756

Bravo AF: 0.481

Asia WGS AF: 0.386 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.24
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1017643; hg19: chr6-156794133;