chr2-4408465-G-A

Variant names:

• chr2-4408465-G-A
• rs2602629
• ENST00000707165.1:n.260-30501G>A

Variant summary

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

The ENST00000707165.1(ENSG00000291325):​n.260-30501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,030 control chromosomes in the GnomAD database, including 26,822 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 0.58 (26822 hom., cov: 32)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 2 publications found

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 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
ENSG00000291325	ENST00000707165.1	n.260-30501G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88099 AN: 151912 Hom.: 26786 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.580 AC: 88200 AN: 152030 Hom.: 26822 Cov.: 32 AF XY: 0.584 AC XY: 43365 AN XY: 74290

African (AFR) AF: 0.753 AC: 31237 AN: 41466

American (AMR) AF: 0.475 AC: 7255 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2145 AN: 3468

East Asian (EAS) AF: 0.751 AC: 3878 AN: 5166

South Asian (SAS) AF: 0.760 AC: 3658 AN: 4810

European-Finnish (FIN) AF: 0.490 AC: 5171 AN: 10550

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33197 AN: 67988

Other (OTH) AF: 0.540 AC: 1141 AN: 2114

Alfa AF: 0.522 Hom.: 75296

Bravo AF: 0.580

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2602629; hg19: chr2-4456055; COSMIC: COSV50574091;