rs1508632

Variant names:

• chr6-54419678-A-G
• rs1508632

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 0.142 in 152,152 control chromosomes in the GnomAD database, including 1,657 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 0.14 (1657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21611 AN: 152034 Hom.: 1657 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0305

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.142 AC: 21617 AN: 152152 Hom.: 1657 Cov.: 32 AF XY: 0.139 AC XY: 10372 AN XY: 74374

African (AFR) AF: 0.110 AC: 4580 AN: 41538

American (AMR) AF: 0.109 AC: 1671 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3464

East Asian (EAS) AF: 0.0302 AC: 156 AN: 5166

South Asian (SAS) AF: 0.142 AC: 685 AN: 4826

European-Finnish (FIN) AF: 0.159 AC: 1690 AN: 10608

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11946 AN: 67958

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.159 Hom.: 1404

Bravo AF: 0.136

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1508632; hg19: chr6-54284476;