rs2660845

Variant names:

• chr12-96044775-G-A
• rs2660845
• ENST00000824362.1:n.272-2843G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-96044775-G-A
• chr12-96044775-G-C

Variant summary

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

The ENST00000824362.1(ENSG00000307169):​n.272-2843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,134 control chromosomes in the GnomAD database, including 36,303 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 0.69 (36303 hom., cov: 33)
• Consequence: ENSG00000307169 ENST00000824362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 42 publications found

Genes affected

ENSG00000307169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 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
ENSG00000307169	ENST00000824362.1	n.272-2843G>A		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824363.1	n.98-8569G>A		intron_variant	Intron 1 of 1
ENSG00000307169	ENST00000824364.1	n.143-2843G>A		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824365.1	n.*50G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104288 AN: 152016 Hom.: 36283 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.686 AC: 104351 AN: 152134 Hom.: 36303 Cov.: 33 AF XY: 0.684 AC XY: 50855 AN XY: 74370

African (AFR) AF: 0.666 AC: 27638 AN: 41492

American (AMR) AF: 0.548 AC: 8382 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2262 AN: 5156

South Asian (SAS) AF: 0.672 AC: 3237 AN: 4816

European-Finnish (FIN) AF: 0.802 AC: 8498 AN: 10602

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49730 AN: 67994

Other (OTH) AF: 0.662 AC: 1401 AN: 2116

Alfa AF: 0.705 Hom.: 133024

Bravo AF: 0.663

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.062
DANN	Benign	0.65
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2660845; hg19: chr12-96438553;