6-36675978-C-T

Variant names:

• chr6-36675978-C-T
• rs9394371

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 0.208 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.208 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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.0848

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.199

Alfa AF: 0.0561 Hom.: 67

Bravo AF: 0.234

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9394371; hg19: chr6-36643755;