2-121904636-T-C

Variant names:

• chr2-121904636-T-C
• rs4241112
• ENST00000657880.2:n.540+1647T>C

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.540+1647T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,152 control chromosomes in the GnomAD database, including 45,403 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 0.77 (45403 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 7 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657880.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286481	ENST00000657880.2		n.540+1647T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117182 AN: 152034 Hom.: 45366 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.771 AC: 117276 AN: 152152 Hom.: 45403 Cov.: 32 AF XY: 0.776 AC XY: 57713 AN XY: 74394

African (AFR) AF: 0.755 AC: 31316 AN: 41482

American (AMR) AF: 0.831 AC: 12718 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2611 AN: 3468

East Asian (EAS) AF: 0.970 AC: 5040 AN: 5194

South Asian (SAS) AF: 0.873 AC: 4203 AN: 4814

European-Finnish (FIN) AF: 0.766 AC: 8112 AN: 10584

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50667 AN: 67992

Other (OTH) AF: 0.774 AC: 1638 AN: 2116

Alfa AF: 0.758 Hom.: 66061

Bravo AF: 0.777

Asia WGS AF: 0.907 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.066
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4241112; hg19: chr2-122662212;