chr6-30424629-C-A

Variant names:

• chr6-30424629-C-A
• rs9261926

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 0.184 in 134,300 control chromosomes in the GnomAD database, including 2,197 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 0.18 (2197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.184 AC: 24701 AN: 134180 Hom.: 2197 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.184 AC: 24716 AN: 134300 Hom.: 2197 Cov.: 31 AF XY: 0.181 AC XY: 11725 AN XY: 64714

African (AFR) AF: 0.257 AC: 9858 AN: 38324

American (AMR) AF: 0.134 AC: 1615 AN: 12074

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 465 AN: 3206

East Asian (EAS) AF: 0.0400 AC: 166 AN: 4154

South Asian (SAS) AF: 0.167 AC: 674 AN: 4038

European-Finnish (FIN) AF: 0.120 AC: 940 AN: 7856

Middle Eastern (MID) AF: 0.105 AC: 28 AN: 266

European-Non Finnish (NFE) AF: 0.170 AC: 10517 AN: 61702

Other (OTH) AF: 0.172 AC: 319 AN: 1854

Alfa AF: 0.151 Hom.: 4674

Bravo AF: 0.171

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.49
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs9261926; hg19: chr6-30392406;