6-99880322-C-T

Variant names:

• chr6-99880322-C-T
• rs4840097

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 0.646 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.646 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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.653

Alfa AF: 0.681 Hom.: 59746

Bravo AF: 0.642

Asia WGS AF: 0.874 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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