rs1347846

Variant names:

• chr12-90266564-G-A
• rs1347846
• ENST00000722829.1:n.404-1224G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-90266564-G-A
• chr12-90266564-G-T

Variant summary

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

The ENST00000722829.1(ENSG00000294335):​n.404-1224G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,856 control chromosomes in the GnomAD database, including 8,314 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 (8314 hom., cov: 32)
• Consequence: ENSG00000294335 ENST00000722829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 4 publications found

Genes affected

ENSG00000294335 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722829.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294335	ENST00000722829.1		n.404-1224G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49818 AN: 151736 Hom.: 8297 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.329 AC: 49885 AN: 151856 Hom.: 8314 Cov.: 32 AF XY: 0.334 AC XY: 24814 AN XY: 74246

African (AFR) AF: 0.308 AC: 12776 AN: 41430

American (AMR) AF: 0.392 AC: 5975 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3464

East Asian (EAS) AF: 0.294 AC: 1518 AN: 5156

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3745 AN: 10558

Middle Eastern (MID) AF: 0.267 AC: 77 AN: 288

European-Non Finnish (NFE) AF: 0.320 AC: 21735 AN: 67880

Other (OTH) AF: 0.313 AC: 660 AN: 2108

Alfa AF: 0.322 Hom.: 13513

Bravo AF: 0.327

Asia WGS AF: 0.424 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.23
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1347846; hg19: chr12-90660341;