rs12046844

Variant names:

• chr1-65772696-G-A
• rs12046844
• ENST00000760442.1:n.342+17535C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-65772696-G-A
• chr1-65772696-G-T

Variant summary

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

The ENST00000760442.1(ENSG00000299098):​n.342+17535C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,068 control chromosomes in the GnomAD database, including 2,866 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 0.18 (2866 hom., cov: 32)
• Consequence: ENSG00000299098 ENST00000760442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579
• Publications: 6 publications found

Genes affected

ENSG00000299098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 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
ENSG00000299098	ENST00000760442.1	n.342+17535C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26631 AN: 151950 Hom.: 2866 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.175 AC: 26639 AN: 152068 Hom.: 2866 Cov.: 32 AF XY: 0.181 AC XY: 13438 AN XY: 74336

African (AFR) AF: 0.0765 AC: 3177 AN: 41504

American (AMR) AF: 0.212 AC: 3241 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2263 AN: 5156

South Asian (SAS) AF: 0.179 AC: 864 AN: 4820

European-Finnish (FIN) AF: 0.298 AC: 3138 AN: 10532

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13059 AN: 67984

Other (OTH) AF: 0.170 AC: 358 AN: 2108

Alfa AF: 0.185 Hom.: 12614

Bravo AF: 0.165

Asia WGS AF: 0.284 AC: 984 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.51
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs12046844; hg19: chr1-66238379;