13-91212418-A-G

Variant names:

• chr13-91212418-A-G
• rs7332514

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 0.0994 in 152,166 control chromosomes in the GnomAD database, including 2,177 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 0.099 (2177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.812
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 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: 0.0993 AC: 15091 AN: 152048 Hom.: 2175 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00687

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0994 AC: 15123 AN: 152166 Hom.: 2177 Cov.: 32 AF XY: 0.0966 AC XY: 7188 AN XY: 74420

African (AFR) AF: 0.317 AC: 13165 AN: 41478

American (AMR) AF: 0.0559 AC: 855 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00750 AC: 26 AN: 3468

East Asian (EAS) AF: 0.0179 AC: 93 AN: 5184

South Asian (SAS) AF: 0.0554 AC: 267 AN: 4822

European-Finnish (FIN) AF: 0.00480 AC: 51 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00687 AC: 467 AN: 67998

Other (OTH) AF: 0.0825 AC: 174 AN: 2110

Alfa AF: 0.0258 Hom.: 63

Bravo AF: 0.113

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	8.8
DANN	Benign	0.60
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs7332514; hg19: chr13-91864672;