rs13232606

Variant names:

• chr7-45931511-A-G
• rs13232606

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 0.033 in 151,884 control chromosomes in the GnomAD database, including 109 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 0.033 (109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0723 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: 0.0331 AC: 5019 AN: 151766 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.00894

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0537

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0791

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0330 AC: 5014 AN: 151884 Hom.: 109 Cov.: 32 AF XY: 0.0324 AC XY: 2408 AN XY: 74242

African (AFR) AF: 0.00891 AC: 370 AN: 41530

American (AMR) AF: 0.0219 AC: 335 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0537 AC: 186 AN: 3466

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5192

South Asian (SAS) AF: 0.0788 AC: 379 AN: 4810

European-Finnish (FIN) AF: 0.0292 AC: 308 AN: 10530

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3328 AN: 67782

Other (OTH) AF: 0.0323 AC: 68 AN: 2106

Alfa AF: 0.0470 Hom.: 94

Bravo AF: 0.0303

Asia WGS AF: 0.0390 AC: 133 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.47
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs13232606; hg19: chr7-45971110;