rs12704796

Variant names:

• chr7-95436538-G-A
• rs12704796

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.174 in 152,114 control chromosomes in the GnomAD database, including 2,610 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 0.17 (2610 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 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: 0.174 AC: 26476 AN: 151996 Hom.: 2607 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.174 AC: 26485 AN: 152114 Hom.: 2610 Cov.: 32 AF XY: 0.177 AC XY: 13144 AN XY: 74344

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.199

Alfa AF: 0.160 Hom.: 257

Bravo AF: 0.182

Asia WGS AF: 0.315 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	2.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12704796; hg19: chr7-95065850;