6-153972653-T-C

Variant names:

• chr6-153972653-T-C
• rs484565

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 0.781 in 152,288 control chromosomes in the GnomAD database, including 46,647 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 0.78 (46647 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 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: 0.781 AC: 118850 AN: 152170 Hom.: 46629 Cov.: 35

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.781 AC: 118913 AN: 152288 Hom.: 46647 Cov.: 35 AF XY: 0.784 AC XY: 58366 AN XY: 74464

African (AFR) AF: 0.824 AC: 34228 AN: 41552

American (AMR) AF: 0.825 AC: 12629 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2337 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3927 AN: 5184

South Asian (SAS) AF: 0.779 AC: 3764 AN: 4834

European-Finnish (FIN) AF: 0.822 AC: 8705 AN: 10596

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

European-Non Finnish (NFE) AF: 0.746 AC: 50747 AN: 68028

Other (OTH) AF: 0.763 AC: 1614 AN: 2114

Alfa AF: 0.757 Hom.: 21104

Bravo AF: 0.784

Asia WGS AF: 0.745 AC: 2593 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	3.5
DANN	Benign	0.25
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs484565; hg19: chr6-154293788;