6-24647001-C-T

Variant names:

• chr6-24647001-C-T
• rs1883592

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 0.703 in 151,986 control chromosomes in the GnomAD database, including 38,086 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 0.70 (38086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.703 AC: 106718 AN: 151868 Hom.: 38058 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.703 AC: 106797 AN: 151986 Hom.: 38086 Cov.: 31 AF XY: 0.699 AC XY: 51922 AN XY: 74266

African (AFR) AF: 0.796 AC: 32975 AN: 41424

American (AMR) AF: 0.767 AC: 11719 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4507 AN: 5158

South Asian (SAS) AF: 0.696 AC: 3357 AN: 4826

European-Finnish (FIN) AF: 0.538 AC: 5666 AN: 10530

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.647 AC: 44015 AN: 67980

Other (OTH) AF: 0.711 AC: 1501 AN: 2110

Alfa AF: 0.669 Hom.: 4200

Bravo AF: 0.724

Asia WGS AF: 0.793 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.44
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1883592; hg19: chr6-24647229;