rs7712189

Variant names:

• chr5-39807487-C-T
• rs7712189

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 0.627 in 152,046 control chromosomes in the GnomAD database, including 31,282 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 0.63 (31282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 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: 0.627 AC: 95282 AN: 151928 Hom.: 31274 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.627 AC: 95328 AN: 152046 Hom.: 31282 Cov.: 32 AF XY: 0.620 AC XY: 46094 AN XY: 74336

African (AFR) AF: 0.476 AC: 19709 AN: 41436

American (AMR) AF: 0.583 AC: 8917 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1175 AN: 5162

South Asian (SAS) AF: 0.658 AC: 3166 AN: 4812

European-Finnish (FIN) AF: 0.679 AC: 7189 AN: 10584

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50391 AN: 67984

Other (OTH) AF: 0.653 AC: 1378 AN: 2110

Alfa AF: 0.710 Hom.: 19874

Bravo AF: 0.609

Asia WGS AF: 0.454 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs7712189; hg19: chr5-39807589;