chr2-212874248-G-A

Variant names:

• chr2-212874248-G-A
• rs7600221
• ENST00000415387.1:n.381+18437C>T

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.381+18437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,082 control chromosomes in the GnomAD database, including 10,052 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 0.35 (10052 hom., cov: 32)
• Consequence: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 5 publications found

Genes affected

ENSG00000273118 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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
ENSG00000273118	ENST00000415387.1	n.381+18437C>T		intron_variant	Intron 4 of 4	3
ENSG00000273118	ENST00000821130.1	n.208-3153C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53297 AN: 151964 Hom.: 10037 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.351 AC: 53328 AN: 152082 Hom.: 10052 Cov.: 32 AF XY: 0.349 AC XY: 25956 AN XY: 74358

African (AFR) AF: 0.256 AC: 10621 AN: 41464

American (AMR) AF: 0.460 AC: 7033 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3258 AN: 5172

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4818

European-Finnish (FIN) AF: 0.244 AC: 2584 AN: 10588

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25326 AN: 67974

Other (OTH) AF: 0.362 AC: 764 AN: 2110

Alfa AF: 0.374 Hom.: 34276

Bravo AF: 0.365

Asia WGS AF: 0.439 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.82
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7600221; hg19: chr2-213738972;