6-153957068-T-C

Variant names:

• chr6-153957068-T-C
• rs613515

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 0.8 in 152,128 control chromosomes in the GnomAD database, including 49,003 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 (49003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.800 AC: 121562 AN: 152012 Hom.: 48978 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.671

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: 0.800 AC: 121634 AN: 152128 Hom.: 49003 Cov.: 32 AF XY: 0.802 AC XY: 59647 AN XY: 74354

African (AFR) AF: 0.889 AC: 36917 AN: 41508

American (AMR) AF: 0.833 AC: 12731 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3899 AN: 5162

South Asian (SAS) AF: 0.788 AC: 3795 AN: 4816

European-Finnish (FIN) AF: 0.823 AC: 8703 AN: 10578

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

European-Non Finnish (NFE) AF: 0.745 AC: 50652 AN: 67980

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

Alfa AF: 0.751 Hom.: 52294

Bravo AF: 0.805

Asia WGS AF: 0.756 AC: 2629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.5
DANN	Benign	0.80
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs613515; hg19: chr6-154278203;