5-148836339-T-C

Variant names:

• chr5-148836339-T-C
• rs17108817
• ENST00000798472.1:n.376+11042T>C

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.376+11042T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,936 control chromosomes in the GnomAD database, including 17,040 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 0.46 (17040 hom., cov: 31)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 3 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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
ENSG00000303969	ENST00000798472.1	n.376+11042T>C		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.349+11042T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69936 AN: 151818 Hom.: 17034 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.460 AC: 69966 AN: 151936 Hom.: 17040 Cov.: 31 AF XY: 0.447 AC XY: 33229 AN XY: 74262

African (AFR) AF: 0.524 AC: 21715 AN: 41408

American (AMR) AF: 0.349 AC: 5322 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3466

East Asian (EAS) AF: 0.0685 AC: 354 AN: 5168

South Asian (SAS) AF: 0.296 AC: 1425 AN: 4810

European-Finnish (FIN) AF: 0.371 AC: 3919 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34036 AN: 67932

Other (OTH) AF: 0.458 AC: 968 AN: 2114

Alfa AF: 0.476 Hom.: 16550

Bravo AF: 0.462

Asia WGS AF: 0.212 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.3
DANN	Benign	0.84
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs17108817; hg19: chr5-148215902;