13-78700335-A-G

Variant names:

• chr13-78700335-A-G
• rs1931035

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 0.799 in 152,182 control chromosomes in the GnomAD database, including 48,962 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 0.80 (48962 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.800 AC: 121585 AN: 152064 Hom.: 48940 Cov.: 33

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.799 AC: 121659 AN: 152182 Hom.: 48962 Cov.: 33 AF XY: 0.802 AC XY: 59634 AN XY: 74386

African (AFR) AF: 0.678 AC: 28136 AN: 41506

American (AMR) AF: 0.823 AC: 12585 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2882 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4661 AN: 5174

South Asian (SAS) AF: 0.874 AC: 4213 AN: 4822

European-Finnish (FIN) AF: 0.825 AC: 8740 AN: 10592

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57810 AN: 68006

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.833 Hom.: 135802

Bravo AF: 0.793

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1931035; hg19: chr13-79274470;