3-180719699-G-T

Variant names:

• chr3-180719699-G-T
• rs1401337
• ENST00000485055.5:n.1458+5816C>A

Variant summary

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

The ENST00000485055.5(ENSG00000285336):​n.1458+5816C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,980 control chromosomes in the GnomAD database, including 29,646 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 0.61 (29646 hom., cov: 32)
• Consequence: ENSG00000285336 ENST00000485055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 6 publications found

Genes affected

ENSG00000285336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928882	NR_109986.1	n.1458+5816C>A		intron_variant	Intron 11 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285336	ENST00000485055.5	n.1458+5816C>A		intron_variant	Intron 11 of 13	1
ENSG00000145075	ENST00000471307.6	n.527+28547C>A		intron_variant	Intron 5 of 6	3
ENSG00000285336	ENST00000495817.1	n.348-8296C>A		intron_variant	Intron 2 of 4	3
ENSG00000145075	ENST00000651576.1	n.441+5816C>A		intron_variant	Intron 2 of 24

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92629 AN: 151862 Hom.: 29589 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.610 AC: 92745 AN: 151980 Hom.: 29646 Cov.: 32 AF XY: 0.609 AC XY: 45222 AN XY: 74286

African (AFR) AF: 0.826 AC: 34282 AN: 41506

American (AMR) AF: 0.524 AC: 7997 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2487 AN: 5164

South Asian (SAS) AF: 0.644 AC: 3110 AN: 4830

European-Finnish (FIN) AF: 0.534 AC: 5619 AN: 10532

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35512 AN: 67894

Other (OTH) AF: 0.578 AC: 1218 AN: 2108

Alfa AF: 0.554 Hom.: 57041

Bravo AF: 0.614

Asia WGS AF: 0.616 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.0
DANN	Benign	0.77
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1401337; hg19: chr3-180437487;