chr13-107065631-G-A

Variant names:

• chr13-107065631-G-A
• rs1927756

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 0.428 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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

African (AFR) AF: 0.276 AC: 11451 AN: 41498

American (AMR) AF: 0.525 AC: 8034 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1784 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2963 AN: 5164

South Asian (SAS) AF: 0.308 AC: 1483 AN: 4818

European-Finnish (FIN) AF: 0.491 AC: 5184 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32598 AN: 67986

Other (OTH) AF: 0.493 AC: 1042 AN: 2112

Alfa AF: 0.444 Hom.: 1987

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
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs1927756; hg19: chr13-107717979;