5-143624040-T-C

Variant names:

• chr5-143624040-T-C
• rs17100498
• ENST00000503323.1:n.104+18309T>C

Variant summary

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

The ENST00000503323.1(ENSG00000249881):​n.104+18309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,008 control chromosomes in the GnomAD database, including 1,156 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 (1156 hom., cov: 32)
• Consequence: ENSG00000249881 ENST00000503323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

ENSG00000249881 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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+18309T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16759 AN: 151890 Hom.: 1155 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.110 AC: 16772 AN: 152008 Hom.: 1156 Cov.: 32 AF XY: 0.108 AC XY: 7990 AN XY: 74294

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.0943

Gnomad4 EAS AF: 0.0298

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.0459

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0689 Hom.: 154

Bravo AF: 0.117

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17100498; hg19: chr5-143003605;