rs1927405

Variant names:

• chr13-77375343-T-C
• rs1927405

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.722

Alfa AF: 0.779 Hom.: 78942

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927405; hg19: chr13-77949478;