rs1927756

Variant names:

• chr13-107065631-G-A
• rs1927756

Your query was ambiguous. Multiple possible variants found:

• chr13-107065631-G-A
• chr13-107065631-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;