rs12994941

Variant names:

• chr2-41723586-T-C
• rs12994941
• ENST00000660664.1:n.110-1101T>C

Variant summary

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

The ENST00000660664.1(ENSG00000287145):​n.110-1101T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,072 control chromosomes in the GnomAD database, including 4,537 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 0.24 (4537 hom., cov: 32)
• Consequence: ENSG00000287145 ENST00000660664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 4 publications found

Genes affected

ENSG00000287145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 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
ENSG00000287145	ENST00000660664.1	n.110-1101T>C		intron_variant	Intron 1 of 2
ENSG00000304630	ENST00000805042.1	n.132-10999A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36804 AN: 151954 Hom.: 4538 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.242 AC: 36818 AN: 152072 Hom.: 4537 Cov.: 32 AF XY: 0.248 AC XY: 18449 AN XY: 74328

African (AFR) AF: 0.222 AC: 9229 AN: 41486

American (AMR) AF: 0.229 AC: 3495 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1790 AN: 5164

South Asian (SAS) AF: 0.361 AC: 1740 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2681 AN: 10554

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15859 AN: 67990

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.238 Hom.: 1627

Bravo AF: 0.238

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12994941; hg19: chr2-41950726;