rs1927756

chr13-107065631-G-Achr13-107065631-G-C

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 0.428 in 152,096 control chromosomes in the GnomAD database, including 14,869 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 0.43 (14869 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65148 AN: 151980 Hom.: 14867 Cov.: 34

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.428 AC: 65173 AN: 152096 Hom.: 14869 Cov.: 34 AF XY: 0.430 AC XY: 31971 AN XY: 74326

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.493

Alfa AF: 0.449 Hom.: 1948

Bravo AF: 0.433

Asia WGS AF: 0.403 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.68
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927756; hg19: chr13-107717979;