6-24647001-C-T

Variant names:

• chr6-24647001-C-T
• rs1883592

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.711

Alfa AF: 0.664 Hom.: 3966

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883592; hg19: chr6-24647229;