5-143625823-C-T

Variant names:

• chr5-143625823-C-T
• rs17100506
• ENST00000503323.1:n.104+20092C>T

Variant summary

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

The ENST00000503323.1(ENSG00000249881):​n.104+20092C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,178 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 32)
• Consequence: ENSG00000249881 ENST00000503323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 3 publications found

Genes affected

ENSG00000249881 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 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
ENSG00000249881	ENST00000503323.1	n.104+20092C>T		intron_variant	Intron 1 of 4	3
ENSG00000249881	ENST00000848438.1	n.502+17515C>T		intron_variant	Intron 2 of 2
ENSG00000249881	ENST00000848439.1	n.187+20092C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16190 AN: 152060 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.106 AC: 16202 AN: 152178 Hom.: 1073 Cov.: 32 AF XY: 0.104 AC XY: 7717 AN XY: 74406

African (AFR) AF: 0.195 AC: 8105 AN: 41490

American (AMR) AF: 0.0777 AC: 1187 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0936 AC: 325 AN: 3472

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5186

South Asian (SAS) AF: 0.0954 AC: 460 AN: 4824

European-Finnish (FIN) AF: 0.0454 AC: 481 AN: 10594

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5203 AN: 68010

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.0458 Hom.: 46

Bravo AF: 0.113

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.74
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17100506; hg19: chr5-143005388;