rs11742519

Variant names:

• chr5-148858745-C-A
• rs11742519
• ENST00000798472.1:n.377-13759C>A

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.377-13759C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,046 control chromosomes in the GnomAD database, including 26,586 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 0.58 (26586 hom., cov: 33)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 4 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=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 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.377-13759C>A		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.350-13759C>A		intron_variant	Intron 3 of 4
ENSG00000303982	ENST00000798634.1	n.153-4952C>A		intron_variant	Intron 1 of 1
ENSG00000303982	ENST00000798635.1	n.135+4629C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88572 AN: 151928 Hom.: 26555 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.583 AC: 88653 AN: 152046 Hom.: 26586 Cov.: 33 AF XY: 0.580 AC XY: 43099 AN XY: 74322

African (AFR) AF: 0.715 AC: 29632 AN: 41440

American (AMR) AF: 0.460 AC: 7040 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3472

East Asian (EAS) AF: 0.429 AC: 2216 AN: 5168

South Asian (SAS) AF: 0.667 AC: 3219 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5381 AN: 10560

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36898 AN: 67968

Other (OTH) AF: 0.607 AC: 1284 AN: 2116

Alfa AF: 0.562 Hom.: 19197

Bravo AF: 0.582

Asia WGS AF: 0.539 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.67
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs11742519; hg19: chr5-148238308;