rs1508632

Variant names:

• chr6-54419678-A-G
• rs1508632

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 0.142 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.142 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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0302

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.147

Alfa AF: 0.163 Hom.: 999

Bravo AF: 0.136

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1508632; hg19: chr6-54284476;