5-112565131-G-A

Variant names:

• chr5-112565131-G-A
• rs7712713

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 0.256 in 151,720 control chromosomes in the GnomAD database, including 5,723 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 0.26 (5723 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.256 AC: 38830 AN: 151602 Hom.: 5710 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.256 AC: 38887 AN: 151720 Hom.: 5723 Cov.: 31 AF XY: 0.253 AC XY: 18762 AN XY: 74096

African (AFR) AF: 0.401 AC: 16568 AN: 41302

American (AMR) AF: 0.206 AC: 3140 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3470

East Asian (EAS) AF: 0.0381 AC: 197 AN: 5174

South Asian (SAS) AF: 0.130 AC: 623 AN: 4798

European-Finnish (FIN) AF: 0.229 AC: 2403 AN: 10476

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14348 AN: 67922

Other (OTH) AF: 0.246 AC: 520 AN: 2110

Alfa AF: 0.221 Hom.: 1462

Bravo AF: 0.266

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.14
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7712713; hg19: chr5-111900828;