6-90510836-C-T

Variant names:

• chr6-90510836-C-T
• rs711264

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 0.242 in 152,118 control chromosomes in the GnomAD database, including 4,745 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 0.24 (4745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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: 0.242 AC: 36823 AN: 152000 Hom.: 4746 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.242 AC: 36816 AN: 152118 Hom.: 4745 Cov.: 32 AF XY: 0.241 AC XY: 17916 AN XY: 74366

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.242

Alfa AF: 0.273 Hom.: 12478

Bravo AF: 0.230

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs711264; hg19: chr6-91220555; COSMIC: COSV65225751;