6-99880322-C-T

Variant names:

• chr6-99880322-C-T
• rs4840097

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 0.646 in 150,728 control chromosomes in the GnomAD database, including 32,833 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 0.65 (32833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.646 AC: 97344 AN: 150608 Hom.: 32810 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.646 AC: 97415 AN: 150728 Hom.: 32833 Cov.: 31 AF XY: 0.656 AC XY: 48317 AN XY: 73692

African (AFR) AF: 0.474 AC: 19280 AN: 40688

American (AMR) AF: 0.754 AC: 11499 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2367 AN: 3434

East Asian (EAS) AF: 0.995 AC: 5145 AN: 5170

South Asian (SAS) AF: 0.802 AC: 3819 AN: 4760

European-Finnish (FIN) AF: 0.691 AC: 7254 AN: 10502

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.680 AC: 45973 AN: 67634

Other (OTH) AF: 0.653 AC: 1368 AN: 2096

Alfa AF: 0.670 Hom.: 93183

Bravo AF: 0.642

Asia WGS AF: 0.874 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4840097; hg19: chr6-100328198; COSMIC: COSV64722394;