2-215455327-C-A

Variant names:

• chr2-215455327-C-A
• rs1250220
• ENST00000447835.2:n.39-1565C>A

Variant summary

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

The ENST00000447835.2(ENSG00000225166):​n.39-1565C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,898 control chromosomes in the GnomAD database, including 21,288 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 0.52 (21288 hom., cov: 32)
• Consequence: ENSG00000225166 ENST00000447835.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 7 publications found

Genes affected

ENSG00000225166 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724849	NR_110607.1	n.20-1565C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225166	ENST00000447835.2	n.39-1565C>A		intron_variant	Intron 1 of 3	5
ENSG00000225166	ENST00000654128.1	n.111+1494C>A		intron_variant	Intron 1 of 3
ENSG00000225166	ENST00000654236.1	n.111+1494C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78913 AN: 151780 Hom.: 21284 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.520 AC: 78948 AN: 151898 Hom.: 21288 Cov.: 32 AF XY: 0.526 AC XY: 39007 AN XY: 74228

African (AFR) AF: 0.447 AC: 18509 AN: 41424

American (AMR) AF: 0.607 AC: 9264 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1955 AN: 3466

East Asian (EAS) AF: 0.924 AC: 4772 AN: 5162

South Asian (SAS) AF: 0.456 AC: 2191 AN: 4810

European-Finnish (FIN) AF: 0.546 AC: 5749 AN: 10524

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34804 AN: 67926

Other (OTH) AF: 0.541 AC: 1144 AN: 2114

Alfa AF: 0.526 Hom.: 28440

Bravo AF: 0.528

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1250220; hg19: chr2-216320050;