chr6-153949988-C-T

Variant names:

• chr6-153949988-C-T
• rs626174

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 0.799 in 151,902 control chromosomes in the GnomAD database, including 48,846 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 0.80 (48846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 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: 0.799 AC: 121296 AN: 151782 Hom.: 48820 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.799 AC: 121370 AN: 151902 Hom.: 48846 Cov.: 32 AF XY: 0.802 AC XY: 59507 AN XY: 74224

African (AFR) AF: 0.888 AC: 36816 AN: 41468

American (AMR) AF: 0.833 AC: 12699 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2322 AN: 3462

East Asian (EAS) AF: 0.757 AC: 3896 AN: 5148

South Asian (SAS) AF: 0.788 AC: 3793 AN: 4812

European-Finnish (FIN) AF: 0.822 AC: 8672 AN: 10550

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50565 AN: 67892

Other (OTH) AF: 0.778 AC: 1645 AN: 2114

Alfa AF: 0.771 Hom.: 5885

Bravo AF: 0.804

Asia WGS AF: 0.756 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs626174; hg19: chr6-154271123;