rs876581

Variant names:

• chr6-36687668-C-T
• rs876581

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 0.13 in 152,064 control chromosomes in the GnomAD database, including 1,905 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 0.13 (1905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.130 AC: 19750 AN: 151946 Hom.: 1904 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19768 AN: 152064 Hom.: 1905 Cov.: 31 AF XY: 0.134 AC XY: 9958 AN XY: 74360

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.127

Alfa AF: 0.119 Hom.: 141

Bravo AF: 0.152

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
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: rs876581; hg19: chr6-36655445;