rs1881140

Variant names:

• chr17-50239511-A-G
• rs1881140
• ENST00000740070.1:n.143-17022A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-50239511-A-G
• chr17-50239511-A-T

Variant summary

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

The ENST00000740070.1(ENSG00000296518):​n.143-17022A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,488 control chromosomes in the GnomAD database, including 18,888 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 0.50 (18888 hom., cov: 30)
• Consequence: ENSG00000296518 ENST00000740070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 6 publications found

Genes affected

ENSG00000296518 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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
ENSG00000296518	ENST00000740070.1	n.143-17022A>G		intron_variant	Intron 1 of 3
ENSG00000296518	ENST00000740071.1	n.132-17001A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.495 AC: 74942 AN: 151372 Hom.: 18870 Cov.: 30

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.495 AC: 74993 AN: 151488 Hom.: 18888 Cov.: 30 AF XY: 0.490 AC XY: 36272 AN XY: 73962

African (AFR) AF: 0.590 AC: 24332 AN: 41270

American (AMR) AF: 0.410 AC: 6229 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1705 AN: 3468

East Asian (EAS) AF: 0.363 AC: 1869 AN: 5144

South Asian (SAS) AF: 0.557 AC: 2670 AN: 4790

European-Finnish (FIN) AF: 0.460 AC: 4827 AN: 10486

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31554 AN: 67830

Other (OTH) AF: 0.505 AC: 1060 AN: 2100

Alfa AF: 0.470 Hom.: 71699

Bravo AF: 0.492

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1881140; hg19: chr17-48316872;