rs7956328

Variant names:

• chr12-124640919-T-A
• rs7956328
• ENST00000767262.1:n.308+27131A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000767262.1(ENSG00000299894):​n.308+27131A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,996 control chromosomes in the GnomAD database, including 5,275 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 (5275 hom., cov: 32)
• Consequence: ENSG00000299894 ENST00000767262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 2 publications found

Genes affected

ENSG00000299894 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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
ENSG00000299894	ENST00000767262.1	n.308+27131A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39251 AN: 151878 Hom.: 5261 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.259 AC: 39299 AN: 151996 Hom.: 5275 Cov.: 32 AF XY: 0.254 AC XY: 18836 AN XY: 74298

African (AFR) AF: 0.267 AC: 11066 AN: 41436

American (AMR) AF: 0.226 AC: 3446 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3462

East Asian (EAS) AF: 0.201 AC: 1039 AN: 5168

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4812

European-Finnish (FIN) AF: 0.219 AC: 2311 AN: 10566

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18533 AN: 67958

Other (OTH) AF: 0.256 AC: 541 AN: 2116

Alfa AF: 0.271 Hom.: 720

Bravo AF: 0.260

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.84
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs7956328; hg19: chr12-125125465;