5-126197437-C-T

Variant names:

• chr5-126197437-C-T
• rs17584191
• ENST00000450613.2:n.71+82294G>A

Variant summary

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

The ENST00000450613.2(ENSG00000248752):​n.71+82294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 141,280 control chromosomes in the GnomAD database, including 4,681 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 0.26 (4681 hom., cov: 27)
• Consequence: ENSG00000248752 ENST00000450613.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 3 publications found

Genes affected

ENSG00000248752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1620-99276G>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000450613.2	n.71+82294G>A		intron_variant	Intron 1 of 2	3
ENSG00000248752	ENST00000651847.1	n.77-2208G>A		intron_variant	Intron 1 of 15
ENSG00000248752	ENST00000781629.1	n.175-2208G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.260 AC: 36749 AN: 141168 Hom.: 4680 Cov.: 27

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.260 AC: 36766 AN: 141280 Hom.: 4681 Cov.: 27 AF XY: 0.261 AC XY: 17733 AN XY: 68070

African (AFR) AF: 0.244 AC: 9304 AN: 38114

American (AMR) AF: 0.271 AC: 3796 AN: 14032

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1194 AN: 3388

East Asian (EAS) AF: 0.134 AC: 600 AN: 4472

South Asian (SAS) AF: 0.187 AC: 802 AN: 4286

European-Finnish (FIN) AF: 0.302 AC: 2486 AN: 8226

Middle Eastern (MID) AF: 0.318 AC: 82 AN: 258

European-Non Finnish (NFE) AF: 0.270 AC: 17727 AN: 65712

Other (OTH) AF: 0.267 AC: 510 AN: 1908

Alfa AF: 0.257 Hom.: 14329

Bravo AF: 0.248

Asia WGS AF: 0.154 AC: 531 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.52
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs17584191; hg19: chr5-125533130;