6-67093411-G-T

Variant names:

• chr6-67093411-G-T
• rs2502248

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 0.635 in 151,872 control chromosomes in the GnomAD database, including 31,417 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 0.63 (31417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.634 AC: 96266 AN: 151754 Hom.: 31371 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.635 AC: 96370 AN: 151872 Hom.: 31417 Cov.: 32 AF XY: 0.636 AC XY: 47234 AN XY: 74218

African (AFR) AF: 0.790 AC: 32750 AN: 41470

American (AMR) AF: 0.620 AC: 9442 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2211 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3097 AN: 5148

South Asian (SAS) AF: 0.662 AC: 3195 AN: 4828

European-Finnish (FIN) AF: 0.553 AC: 5840 AN: 10564

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37667 AN: 67850

Other (OTH) AF: 0.647 AC: 1363 AN: 2108

Alfa AF: 0.603 Hom.: 3707

Bravo AF: 0.644

Asia WGS AF: 0.657 AC: 2283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.56
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2502248; hg19: chr6-67803304; COSMIC: COSV69401077;