6-36675978-C-T

Variant names:

• chr6-36675978-C-T
• rs9394371

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 0.208 in 152,022 control chromosomes in the GnomAD database, including 4,059 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 0.21 (4059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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: 0.208 AC: 31633 AN: 151904 Hom.: 4050 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.208 AC: 31676 AN: 152022 Hom.: 4059 Cov.: 32 AF XY: 0.209 AC XY: 15565 AN XY: 74308

African (AFR) AF: 0.313 AC: 12971 AN: 41430

American (AMR) AF: 0.302 AC: 4608 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2119 AN: 5170

South Asian (SAS) AF: 0.119 AC: 575 AN: 4818

European-Finnish (FIN) AF: 0.118 AC: 1246 AN: 10566

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9279 AN: 67972

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.0869 Hom.: 136

Bravo AF: 0.234

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.44
PhyloP100		0.88
PromoterAI		-0.00060	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9394371; hg19: chr6-36643755;