3-98536548-T-G

Variant names:

• chr3-98536548-T-G
• rs1350790
• ENST00000512905.6:n.*71-15106A>C

Variant summary

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

The ENST00000512905.6(ENSG00000285635):​n.*71-15106A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,114 control chromosomes in the GnomAD database, including 27,550 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 0.59 (27550 hom., cov: 33)
• Consequence: ENSG00000285635 ENST00000512905.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.861
• Publications: 5 publications found

Genes affected

ENSG00000285635 (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 (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512905.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285635	ENST00000512905.6	TSL:5	n.*71-15106A>C		intron	N/A	ENSP00000425880.1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89420 AN: 151996 Hom.: 27551 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.588 AC: 89440 AN: 152114 Hom.: 27550 Cov.: 33 AF XY: 0.593 AC XY: 44085 AN XY: 74364

African (AFR) AF: 0.406 AC: 16822 AN: 41478

American (AMR) AF: 0.693 AC: 10597 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4338 AN: 5172

South Asian (SAS) AF: 0.612 AC: 2953 AN: 4824

European-Finnish (FIN) AF: 0.652 AC: 6900 AN: 10580

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.646 AC: 43928 AN: 67990

Other (OTH) AF: 0.603 AC: 1274 AN: 2112

Alfa AF: 0.628 Hom.: 120395

Bravo AF: 0.585

Asia WGS AF: 0.648 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.4
DANN	Benign	0.81
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs1350790; hg19: chr3-98255392;