3-98315682-G-A

Variant names:

• chr3-98315682-G-A
• rs1497546
• ENST00000508616.1:n.149+3674G>A

Variant summary

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

The ENST00000508616.1(ENSG00000251088):​n.149+3674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,184 control chromosomes in the GnomAD database, including 1,263 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 0.086 (1263 hom., cov: 32)
• Consequence: ENSG00000251088 ENST00000508616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 9 publications found

Genes affected

ENSG00000251088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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
ENSG00000251088	ENST00000508616.1	n.149+3674G>A		intron_variant	Intron 2 of 3	1
ENSG00000289509	ENST00000688712.2	n.128+9411C>T		intron_variant	Intron 1 of 2
ENSG00000289509	ENST00000689242.2	n.182+9411C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13104 AN: 152066 Hom.: 1262 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0863 AC: 13130 AN: 152184 Hom.: 1263 Cov.: 32 AF XY: 0.0841 AC XY: 6259 AN XY: 74392

African (AFR) AF: 0.236 AC: 9788 AN: 41454

American (AMR) AF: 0.0395 AC: 605 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3468

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5184

South Asian (SAS) AF: 0.0475 AC: 229 AN: 4824

European-Finnish (FIN) AF: 0.0312 AC: 331 AN: 10604

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0254 AC: 1728 AN: 68032

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0473 Hom.: 1295

Bravo AF: 0.0935

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.41
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1497546; hg19: chr3-98034526;