6-24647879-G-C

Variant names:

• chr6-24647879-G-C
• rs1555090

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 151,992 control chromosomes in the GnomAD database, including 38,156 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 (38156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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: 106835 AN: 151874 Hom.: 38128 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.703 AC: 106914 AN: 151992 Hom.: 38156 Cov.: 31 AF XY: 0.700 AC XY: 52001 AN XY: 74280

African (AFR) AF: 0.796 AC: 33010 AN: 41478

American (AMR) AF: 0.767 AC: 11720 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2161 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4521 AN: 5168

South Asian (SAS) AF: 0.696 AC: 3349 AN: 4810

European-Finnish (FIN) AF: 0.541 AC: 5692 AN: 10524

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44002 AN: 67944

Other (OTH) AF: 0.712 AC: 1507 AN: 2116

Alfa AF: 0.664 Hom.: 3967

Bravo AF: 0.725

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	-0.96
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1555090; hg19: chr6-24648107;