rs13192471

Variant names:

• chr6-32703326-T-C
• rs13192471

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 0.186 in 152,010 control chromosomes in the GnomAD database, including 2,930 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 0.19 (2930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• Publications: 78 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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: 0.186 AC: 28205 AN: 151890 Hom.: 2923 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.186 AC: 28251 AN: 152010 Hom.: 2930 Cov.: 31 AF XY: 0.192 AC XY: 14268 AN XY: 74324

African (AFR) AF: 0.227 AC: 9400 AN: 41398

American (AMR) AF: 0.213 AC: 3249 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3466

East Asian (EAS) AF: 0.134 AC: 695 AN: 5184

South Asian (SAS) AF: 0.106 AC: 513 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3373 AN: 10528

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9835 AN: 68008

Other (OTH) AF: 0.186 AC: 392 AN: 2106

Alfa AF: 0.154 Hom.: 6796

Bravo AF: 0.182

Asia WGS AF: 0.154 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	12
DANN	Benign	0.37
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs13192471; hg19: chr6-32671103;