chr13-77375343-T-C

Variant names:

• chr13-77375343-T-C
• rs1927405

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 0.666 in 152,184 control chromosomes in the GnomAD database, including 35,934 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 0.67 (35934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.791 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: 0.667 AC: 101370 AN: 152068 Hom.: 35930 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.666 AC: 101400 AN: 152184 Hom.: 35934 Cov.: 32 AF XY: 0.660 AC XY: 49102 AN XY: 74408

African (AFR) AF: 0.417 AC: 17293 AN: 41492

American (AMR) AF: 0.708 AC: 10815 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3039 AN: 3470

East Asian (EAS) AF: 0.623 AC: 3233 AN: 5188

South Asian (SAS) AF: 0.563 AC: 2714 AN: 4824

European-Finnish (FIN) AF: 0.720 AC: 7633 AN: 10600

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54164 AN: 68008

Other (OTH) AF: 0.722 AC: 1525 AN: 2112

Alfa AF: 0.749 Hom.: 119943

Bravo AF: 0.660

Asia WGS AF: 0.611 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.74
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1927405; hg19: chr13-77949478;