rs12704796

Variant names:

• chr7-95436538-G-A
• rs12704796
• ENST00000818771.1:n.639+933G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000818771.1(ENSG00000233942):​n.639+933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000233942 ENST00000818771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 5 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000233942	ENST00000818771.1	n.639+933G>A		intron_variant	Intron 2 of 8
ENSG00000233942	ENST00000818772.1	n.464-34154G>A		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818773.1	n.553+933G>A		intron_variant	Intron 2 of 5
ENSG00000233942	ENST00000818774.1	n.118+933G>A		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.121 AC: 5025 AN: 41490

American (AMR) AF: 0.253 AC: 3861 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 608 AN: 3464

East Asian (EAS) AF: 0.373 AC: 1930 AN: 5174

South Asian (SAS) AF: 0.257 AC: 1241 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1440 AN: 10572

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11795 AN: 67994

Other (OTH) AF: 0.199 AC: 419 AN: 2110

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12704796; hg19: chr7-95065850;