5-143624040-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503323.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249881	ENST00000503323.1	TSL:3	n.104+18309T>C		intron	N/A
	ENSG00000249881	ENST00000848438.1		n.502+15732T>C		intron	N/A
	ENSG00000249881	ENST00000848439.1		n.187+18309T>C		intron	N/A

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

African (AFR) AF: 0.206 AC: 8522 AN: 41454

American (AMR) AF: 0.0798 AC: 1220 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0943 AC: 327 AN: 3468

East Asian (EAS) AF: 0.0298 AC: 154 AN: 5168

South Asian (SAS) AF: 0.0992 AC: 477 AN: 4810

European-Finnish (FIN) AF: 0.0459 AC: 484 AN: 10552

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0779 AC: 5293 AN: 67968

Other (OTH) AF: 0.104 AC: 219 AN: 2104

Alfa AF: 0.0794 Hom.: 289

Bravo AF: 0.117

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.48
PhyloP100		-1.5
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: rs17100498; hg19: chr5-143003605;