chr3-172844744-G-T

Variant names:

• chr3-172844744-G-T
• rs9290452
• ENST00000774912.1:n.48-453G>T

Variant summary

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

The ENST00000774912.1(ENSG00000300898):​n.48-453G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,180 control chromosomes in the GnomAD database, including 1,875 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 0.12 (1875 hom., cov: 33)
• Consequence: ENSG00000300898 ENST00000774912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 6 publications found

Genes affected

ENSG00000300898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 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
ENSG00000300898	ENST00000774912.1	n.48-453G>T		intron_variant	Intron 1 of 4
ENSG00000300898	ENST00000774913.1	n.173-453G>T		intron_variant	Intron 2 of 5
ENSG00000300898	ENST00000774914.1	n.73-453G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18945 AN: 152062 Hom.: 1873 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.125 AC: 18975 AN: 152180 Hom.: 1875 Cov.: 33 AF XY: 0.124 AC XY: 9209 AN XY: 74408

African (AFR) AF: 0.262 AC: 10874 AN: 41462

American (AMR) AF: 0.0856 AC: 1309 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3472

East Asian (EAS) AF: 0.106 AC: 551 AN: 5182

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4824

European-Finnish (FIN) AF: 0.0234 AC: 248 AN: 10604

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0610 AC: 4150 AN: 68026

Other (OTH) AF: 0.122 AC: 257 AN: 2114

Alfa AF: 0.0886 Hom.: 517

Bravo AF: 0.133

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9290452; hg19: chr3-172562534;