rs983037

Variant names:

• chr2-12940094-A-C
• rs983037
• ENST00000655303.2:n.1842-24167T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-12940094-A-C
• chr2-12940094-A-G

Variant summary

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

The ENST00000655303.2(ENSG00000225649):​n.1842-24167T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,830 control chromosomes in the GnomAD database, including 6,304 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 0.27 (6304 hom., cov: 32)
• Consequence: ENSG00000225649 ENST00000655303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 3 publications found

Genes affected

ENSG00000225649 (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 (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655303.2. 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
	ENSG00000225649	ENST00000655303.2		n.1842-24167T>G		intron	N/A
	ENSG00000225649	ENST00000663507.1		n.237-24167T>G		intron	N/A
	ENSG00000225649	ENST00000664540.1		n.570-24167T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41636 AN: 151712 Hom.: 6301 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.274 AC: 41644 AN: 151830 Hom.: 6304 Cov.: 32 AF XY: 0.270 AC XY: 20043 AN XY: 74184

African (AFR) AF: 0.191 AC: 7908 AN: 41492

American (AMR) AF: 0.221 AC: 3373 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1260 AN: 3464

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5180

South Asian (SAS) AF: 0.176 AC: 849 AN: 4812

European-Finnish (FIN) AF: 0.357 AC: 3759 AN: 10534

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23218 AN: 67772

Other (OTH) AF: 0.272 AC: 574 AN: 2108

Alfa AF: 0.318 Hom.: 3991

Bravo AF: 0.260

Asia WGS AF: 0.109 AC: 379 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.82
PhyloP100		-0.74

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs983037;

hg19: chr2-13080220;