rs2602629

Positions:

• chr2-4408465-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707165.1(ENSG00000291325):​n.260-30501G>A variant causes a intron, non coding transcript 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: ENST00000707165.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707165.1	n.260-30501G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.540

Alfa AF: 0.508 Hom.: 30241

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

Splicing

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

Publications

LitVar

Other links and lift over

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