rs987858

Variant names:

• chr3-16049413-T-A
• rs987858
• ENST00000691919.3:n.259-87978T>A

Variant summary

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

The ENST00000691919.3(ENSG00000287042):​n.259-87978T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,160 control chromosomes in the GnomAD database, including 5,482 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 0.26 (5482 hom., cov: 33)
• Consequence: ENSG00000287042 ENST00000691919.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• Publications: 1 publications found

Genes affected

ENSG00000287042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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
ENSG00000287042	ENST00000691919.3	n.259-87978T>A		intron_variant	Intron 3 of 3
ENSG00000287042	ENST00000702385.2	n.293-87978T>A		intron_variant	Intron 3 of 3
ENSG00000287042	ENST00000702609.2	n.217-87978T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40057 AN: 152042 Hom.: 5480 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.263 AC: 40075 AN: 152160 Hom.: 5482 Cov.: 33 AF XY: 0.255 AC XY: 18999 AN XY: 74396

African (AFR) AF: 0.319 AC: 13226 AN: 41490

American (AMR) AF: 0.236 AC: 3617 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3472

East Asian (EAS) AF: 0.131 AC: 677 AN: 5186

South Asian (SAS) AF: 0.247 AC: 1193 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1557 AN: 10600

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18077 AN: 67980

Other (OTH) AF: 0.283 AC: 596 AN: 2106

Alfa AF: 0.259 Hom.: 636

Bravo AF: 0.272

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs987858; hg19: chr3-16090920;