chr6-36687668-C-T

Variant names:

• chr6-36687668-C-T
• rs876581

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 0.13 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.188 AC: 7771 AN: 41410

American (AMR) AF: 0.217 AC: 3319 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2373 AN: 5182

South Asian (SAS) AF: 0.112 AC: 539 AN: 4822

European-Finnish (FIN) AF: 0.0600 AC: 635 AN: 10586

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4443 AN: 68000

Other (OTH) AF: 0.127 AC: 268 AN: 2112

Alfa AF: 0.0954 Hom.: 4825

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
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs876581; hg19: chr6-36655445;