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. Variant got -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

Genes affected

ENSG00000225649 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000225649	ENST00000655303.2	n.1842-24167T>G		intron_variant	Intron 3 of 4
ENSG00000225649	ENST00000663507.1	n.237-24167T>G		intron_variant	Intron 2 of 6
ENSG00000225649	ENST00000664540.1	n.570-24167T>G		intron_variant	Intron 4 of 5

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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.272

Alfa AF: 0.316 Hom.: 3485

Bravo AF: 0.260

Asia WGS AF: 0.109 AC: 379 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs983037; hg19: chr2-13080220;