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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450613.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248752	ENST00000450613.2	TSL:3	n.71+82294G>A		intron	N/A
	ENSG00000248752	ENST00000651847.1		n.77-2208G>A		intron	N/A
	ENSG00000248752	ENST00000781629.1		n.175-2208G>A		intron	N/A

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 v4.9

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;