rs252706

Variant names:

• chr5-111081162-G-A
• rs252706
• ENST00000507269.3:n.212+3196C>T

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.212+3196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0299 in 152,224 control chromosomes in the GnomAD database, including 329 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 0.030 (329 hom., cov: 32)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 4 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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
ENSG00000253613	ENST00000507269.3	n.212+3196C>T		intron_variant	Intron 2 of 3	5
ENSG00000253613	ENST00000741219.1	n.137-4117C>T		intron_variant	Intron 1 of 2
ENSG00000253613	ENST00000741220.1	n.137-4778C>T		intron_variant	Intron 1 of 1
ENSG00000253613	ENST00000741221.1	n.100-4117C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0299 AC: 4554 AN: 152106 Hom.: 330 Cov.: 32

Gnomad AFR AF: 0.00560

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0233

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0299 AC: 4552 AN: 152224 Hom.: 329 Cov.: 32 AF XY: 0.0327 AC XY: 2433 AN XY: 74426

African (AFR) AF: 0.00558 AC: 232 AN: 41548

American (AMR) AF: 0.0235 AC: 359 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5170

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4832

European-Finnish (FIN) AF: 0.0316 AC: 335 AN: 10608

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0224 AC: 1522 AN: 67992

Other (OTH) AF: 0.0374 AC: 79 AN: 2110

Alfa AF: 0.0310 Hom.: 448

Bravo AF: 0.0303

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.25
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs252706; hg19: chr5-110416860; COSMIC: COSV65663382;