rs2165738

Variant names:

• chr2-24469940-C-G
• rs2165738
• ENST00000826690.1:n.446+3116C>G

Variant summary

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

The ENST00000826690.1(ENSG00000286829):​n.446+3116C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,032 control chromosomes in the GnomAD database, including 31,114 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 0.61 (31114 hom., cov: 32)
• Consequence: ENSG00000286829 ENST00000826690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 30 publications found

Genes affected

ENSG00000286829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 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
ENSG00000286829	ENST00000826690.1	n.446+3116C>G		intron_variant	Intron 4 of 5
ENSG00000286829	ENST00000826691.1	n.468-3073C>G		intron_variant	Intron 4 of 4
ENSG00000286829	ENST00000826692.1	n.255-3073C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92640 AN: 151914 Hom.: 31100 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.610 AC: 92679 AN: 152032 Hom.: 31114 Cov.: 32 AF XY: 0.613 AC XY: 45547 AN XY: 74326

African (AFR) AF: 0.306 AC: 12660 AN: 41434

American (AMR) AF: 0.716 AC: 10938 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3392 AN: 5172

South Asian (SAS) AF: 0.669 AC: 3227 AN: 4822

European-Finnish (FIN) AF: 0.743 AC: 7842 AN: 10558

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49855 AN: 67978

Other (OTH) AF: 0.640 AC: 1351 AN: 2110

Alfa AF: 0.710 Hom.: 21667

Bravo AF: 0.595

Asia WGS AF: 0.665 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.68
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2165738; hg19: chr2-24692809;