rs1863196

Variant names:

• chr2-165701000-A-G
• rs1863196
• ENST00000714418.1:n.486+2037T>C

Variant summary

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

The ENST00000714418.1(ENSG00000293576):​n.486+2037T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,046 control chromosomes in the GnomAD database, including 12,717 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 0.39 (12717 hom., cov: 32)
• Consequence: ENSG00000293576 ENST00000714418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 7 publications found

Genes affected

ENSG00000293576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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
ENSG00000293576	ENST00000714418.1	n.486+2037T>C		intron_variant	Intron 5 of 5
ENSG00000293576	ENST00000715190.1	n.649+2037T>C		intron_variant	Intron 6 of 6
ENSG00000293576	ENST00000715191.1	n.620+2037T>C		intron_variant	Intron 6 of 6
ENSG00000293576	ENST00000715192.1	n.457-903T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58847 AN: 151928 Hom.: 12710 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.387 AC: 58867 AN: 152046 Hom.: 12717 Cov.: 32 AF XY: 0.391 AC XY: 29028 AN XY: 74318

African (AFR) AF: 0.201 AC: 8353 AN: 41468

American (AMR) AF: 0.356 AC: 5441 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1761 AN: 5170

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4814

European-Finnish (FIN) AF: 0.522 AC: 5517 AN: 10562

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33098 AN: 67970

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.393 Hom.: 3686

Bravo AF: 0.363

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1863196; hg19: chr2-166557510;