6-24646991-C-A

Variant names:

• chr6-24646991-C-A
• rs9467247

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 0.225 in 152,026 control chromosomes in the GnomAD database, including 4,832 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 0.23 (4832 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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: 0.225 AC: 34216 AN: 151908 Hom.: 4830 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.225 AC: 34246 AN: 152026 Hom.: 4832 Cov.: 33 AF XY: 0.231 AC XY: 17147 AN XY: 74320

African (AFR) AF: 0.207 AC: 8592 AN: 41446

American (AMR) AF: 0.368 AC: 5624 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3252 AN: 5154

South Asian (SAS) AF: 0.428 AC: 2062 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1309 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11807 AN: 67994

Other (OTH) AF: 0.241 AC: 507 AN: 2108

Alfa AF: 0.0733 Hom.: 86

Bravo AF: 0.240

Asia WGS AF: 0.507 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9467247; hg19: chr6-24647219;