2-212729246-G-T

Variant names:

• chr2-212729246-G-T
• rs7565158
• ENST00000415387.1:n.382-147838C>A

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.382-147838C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,716 control chromosomes in the GnomAD database, including 26,754 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 0.57 (26754 hom., cov: 30)
• Consequence: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273118	ENST00000415387.1	TSL:3	n.382-147838C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86840 AN: 151598 Hom.: 26747 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.573 AC: 86868 AN: 151716 Hom.: 26754 Cov.: 30 AF XY: 0.569 AC XY: 42173 AN XY: 74132

African (AFR) AF: 0.344 AC: 14203 AN: 41310

American (AMR) AF: 0.543 AC: 8271 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2304 AN: 5154

South Asian (SAS) AF: 0.529 AC: 2538 AN: 4800

European-Finnish (FIN) AF: 0.721 AC: 7575 AN: 10502

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47380 AN: 67934

Other (OTH) AF: 0.596 AC: 1256 AN: 2106

Alfa AF: 0.653 Hom.: 104757

Bravo AF: 0.546

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.74
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7565158;

hg19: chr2-213593970;