rs13204672

Variant names:

• chr6-32615019-A-G
• rs13204672

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 0.124 in 152,214 control chromosomes in the GnomAD database, including 1,324 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 0.12 (1324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 18 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 (SAS) allele frequency at 95% confidence interval = 0.159 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: 0.124 AC: 18883 AN: 152096 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.124 AC: 18875 AN: 152214 Hom.: 1324 Cov.: 32 AF XY: 0.119 AC XY: 8888 AN XY: 74428

African (AFR) AF: 0.119 AC: 4958 AN: 41522

American (AMR) AF: 0.111 AC: 1691 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3470

East Asian (EAS) AF: 0.0424 AC: 220 AN: 5188

South Asian (SAS) AF: 0.168 AC: 811 AN: 4820

European-Finnish (FIN) AF: 0.0551 AC: 585 AN: 10608

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9603 AN: 68002

Other (OTH) AF: 0.146 AC: 309 AN: 2110

Alfa AF: 0.133 Hom.: 1210

Bravo AF: 0.131

Asia WGS AF: 0.0800 AC: 276 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	1.5
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13204672; hg19: chr6-32582796;