13-37561466-G-C

Variant names:

• chr13-37561466-G-C
• rs7994218

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 0.708 in 152,106 control chromosomes in the GnomAD database, including 38,508 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 0.71 (38508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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: 0.708 AC: 107549 AN: 151990 Hom.: 38472 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.708 AC: 107633 AN: 152106 Hom.: 38508 Cov.: 32 AF XY: 0.716 AC XY: 53268 AN XY: 74368

African (AFR) AF: 0.791 AC: 32825 AN: 41510

American (AMR) AF: 0.710 AC: 10856 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4316 AN: 5160

South Asian (SAS) AF: 0.671 AC: 3233 AN: 4820

European-Finnish (FIN) AF: 0.754 AC: 7960 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44343 AN: 67968

Other (OTH) AF: 0.690 AC: 1458 AN: 2114

Alfa AF: 0.678 Hom.: 4381

Bravo AF: 0.707

Asia WGS AF: 0.740 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.067
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7994218; hg19: chr13-38135603;