rs181781

Variant names:

• chr5-132059422-G-A
• rs181781
• ENST00000791953.1:n.85+3218C>T

Variant summary

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

The ENST00000791953.1(ENSG00000303119):​n.85+3218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,122 control chromosomes in the GnomAD database, including 959 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 0.093 (959 hom., cov: 32)
• Consequence: ENSG00000303119 ENST00000791953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 20 publications found

Genes affected

ENSG00000303119 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379174	XR_001742531.2	n.211+2049C>T		intron_variant	Intron 2 of 4
LOC105379174	XR_948784.3	n.398+2049C>T		intron_variant	Intron 2 of 2
LOC105379174	XR_948785.3	n.228+2049C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303119	ENST00000791953.1	n.85+3218C>T		intron_variant	Intron 1 of 2
ENSG00000303119	ENST00000791954.1	n.248+2049C>T		intron_variant	Intron 2 of 2
ENSG00000303119	ENST00000791955.1	n.236+2049C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14209 AN: 152004 Hom.: 962 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0944

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

GnomAD4 genome AF: 0.0934 AC: 14207 AN: 152122 Hom.: 959 Cov.: 32 AF XY: 0.0975 AC XY: 7254 AN XY: 74368

African (AFR) AF: 0.0270 AC: 1122 AN: 41516

American (AMR) AF: 0.0769 AC: 1176 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5152

South Asian (SAS) AF: 0.109 AC: 526 AN: 4816

European-Finnish (FIN) AF: 0.166 AC: 1753 AN: 10584

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7163 AN: 67978

Other (OTH) AF: 0.0958 AC: 202 AN: 2108

Alfa AF: 0.0945 Hom.: 1146

Bravo AF: 0.0836

Asia WGS AF: 0.191 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs181781; hg19: chr5-131395115;