2-239765595-T-G

Variant names:

• chr2-239765595-T-G
• rs10207060
• ENST00000407524.1:n.73+2663T>G

Variant summary

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

The ENST00000407524.1(ENSG00000220256):​n.73+2663T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,964 control chromosomes in the GnomAD database, including 20,771 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 0.51 (20771 hom., cov: 32)
• Consequence: ENSG00000220256 ENST00000407524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 8 publications found

Genes affected

ENSG00000220256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407524.1. 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
	LOC150935	NR_037808.1		n.73+2663T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000220256	ENST00000407524.1	TSL:2	n.73+2663T>G		intron	N/A
	ENSG00000220256	ENST00000786286.1		n.243+2663T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78162 AN: 151846 Hom.: 20755 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.515 AC: 78227 AN: 151964 Hom.: 20771 Cov.: 32 AF XY: 0.517 AC XY: 38400 AN XY: 74258

African (AFR) AF: 0.612 AC: 25359 AN: 41426

American (AMR) AF: 0.521 AC: 7960 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4086 AN: 5146

South Asian (SAS) AF: 0.508 AC: 2445 AN: 4814

European-Finnish (FIN) AF: 0.466 AC: 4915 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30563 AN: 67954

Other (OTH) AF: 0.511 AC: 1079 AN: 2110

Alfa AF: 0.475 Hom.: 45367

Bravo AF: 0.525

Asia WGS AF: 0.600 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.20
PhyloP100		-0.73

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: rs10207060;

hg19: chr2-240687289;