2-239496966-G-A

Variant names:

• chr2-239496966-G-A
• rs6743931
• ENST00000659636.1:n.318-32660G>A

Variant summary

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

The ENST00000659636.1(ENSG00000286525):​n.318-32660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 150,812 control chromosomes in the GnomAD database, including 2,207 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 0.16 (2207 hom., cov: 33)
• Consequence: ENSG00000286525 ENST00000659636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 9 publications found

Genes affected

ENSG00000286525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286525	ENST00000659636.1		n.318-32660G>A		intron	N/A
	ENSG00000288082	ENST00000776286.1		n.175-530C>T		intron	N/A
	ENSG00000288082	ENST00000776287.1		n.69-530C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24833 AN: 150692 Hom.: 2207 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00743

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.165 AC: 24847 AN: 150812 Hom.: 2207 Cov.: 33 AF XY: 0.162 AC XY: 11912 AN XY: 73562

African (AFR) AF: 0.221 AC: 9032 AN: 40954

American (AMR) AF: 0.101 AC: 1533 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3468

East Asian (EAS) AF: 0.00745 AC: 38 AN: 5102

South Asian (SAS) AF: 0.146 AC: 697 AN: 4790

European-Finnish (FIN) AF: 0.182 AC: 1872 AN: 10272

Middle Eastern (MID) AF: 0.135 AC: 39 AN: 288

European-Non Finnish (NFE) AF: 0.159 AC: 10755 AN: 67812

Other (OTH) AF: 0.159 AC: 333 AN: 2096

Alfa AF: 0.154 Hom.: 9099

Bravo AF: 0.160

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.62
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6743931; hg19: chr2-240418660;