rs1795708

Variant names:

• chr12-58356897-T-C
• rs1795708

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 0.328 in 152,080 control chromosomes in the GnomAD database, including 8,364 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 0.33 (8364 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.345 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: 0.328 AC: 49823 AN: 151962 Hom.: 8365 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.328 AC: 49833 AN: 152080 Hom.: 8364 Cov.: 33 AF XY: 0.332 AC XY: 24642 AN XY: 74324

African (AFR) AF: 0.291 AC: 12053 AN: 41488

American (AMR) AF: 0.246 AC: 3765 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1763 AN: 5168

South Asian (SAS) AF: 0.342 AC: 1652 AN: 4824

European-Finnish (FIN) AF: 0.441 AC: 4657 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23676 AN: 67946

Other (OTH) AF: 0.320 AC: 677 AN: 2116

Alfa AF: 0.332 Hom.: 32754

Bravo AF: 0.308

Asia WGS AF: 0.299 AC: 1043 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	13
DANN	Benign	0.81
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1795708; hg19: chr12-58750680;