6-153966817-T-C

Variant names:

• chr6-153966817-T-C
• rs282103

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 0.751 in 152,124 control chromosomes in the GnomAD database, including 43,092 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 0.75 (43092 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.806 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: 0.751 AC: 114129 AN: 152006 Hom.: 43068 Cov.: 33

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.751 AC: 114192 AN: 152124 Hom.: 43092 Cov.: 33 AF XY: 0.755 AC XY: 56193 AN XY: 74384

African (AFR) AF: 0.717 AC: 29729 AN: 41490

American (AMR) AF: 0.818 AC: 12500 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3468

East Asian (EAS) AF: 0.757 AC: 3910 AN: 5166

South Asian (SAS) AF: 0.789 AC: 3810 AN: 4828

European-Finnish (FIN) AF: 0.823 AC: 8708 AN: 10580

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50668 AN: 67992

Other (OTH) AF: 0.750 AC: 1581 AN: 2108

Alfa AF: 0.737 Hom.: 5133

Bravo AF: 0.750

Asia WGS AF: 0.746 AC: 2596 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	0.013
DANN	Benign	0.24
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs282103; hg19: chr6-154287952;