6-100466841-C-T

Variant names:

• chr6-100466841-C-T
• rs4840133

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 0.478 in 151,872 control chromosomes in the GnomAD database, including 17,670 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 0.48 (17670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 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: 0.478 AC: 72584 AN: 151752 Hom.: 17662 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.478 AC: 72611 AN: 151872 Hom.: 17670 Cov.: 32 AF XY: 0.479 AC XY: 35562 AN XY: 74194

African (AFR) AF: 0.419 AC: 17345 AN: 41388

American (AMR) AF: 0.429 AC: 6548 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1705 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1567 AN: 5150

South Asian (SAS) AF: 0.644 AC: 3087 AN: 4792

European-Finnish (FIN) AF: 0.525 AC: 5538 AN: 10546

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35281 AN: 67950

Other (OTH) AF: 0.487 AC: 1025 AN: 2104

Alfa AF: 0.370 Hom.: 1025

Bravo AF: 0.461

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4840133; hg19: chr6-100914717; COSMIC: COSV53490290;