6-90510836-C-T

Variant names:

• chr6-90510836-C-T
• rs711264

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 0.242 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.194 AC: 8052 AN: 41512

American (AMR) AF: 0.184 AC: 2813 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3470

East Asian (EAS) AF: 0.102 AC: 526 AN: 5182

South Asian (SAS) AF: 0.159 AC: 766 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3403 AN: 10546

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19561 AN: 67984

Other (OTH) AF: 0.242 AC: 511 AN: 2112

Alfa AF: 0.267 Hom.: 25111

Bravo AF: 0.230

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.30
PhyloP100		0.13

Splicing

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

Other links and lift over

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