3-98536548-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285635 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000285635	ENST00000512905.6	n.*71-15106A>C		intron_variant	Intron 3 of 3	5		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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.603

Alfa AF: 0.635 Hom.: 57185

Bravo AF: 0.585

Asia WGS AF: 0.648 AC: 2250 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	6.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350790; hg19: chr3-98255392;