rs75316749

Variant names:

• chr3-169043635-A-G
• rs75316749
• ENST00000791974.1:n.363-11827T>C

Variant summary

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

The ENST00000791974.1(ENSG00000303122):​n.363-11827T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0431 in 152,262 control chromosomes in the GnomAD database, including 158 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 0.043 (158 hom., cov: 32)
• Consequence: ENSG00000303122 ENST00000791974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 4 publications found

Genes affected

ENSG00000303122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986051	XR_001740574.2	n.80-11827T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303122	ENST00000791974.1	n.363-11827T>C		intron_variant	Intron 3 of 4
ENSG00000303122	ENST00000791976.1	n.157+6083T>C		intron_variant	Intron 1 of 2
ENSG00000303137	ENST00000792140.1	n.107+1488A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 6562 AN: 152144 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.00868

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0431 AC: 6559 AN: 152262 Hom.: 158 Cov.: 32 AF XY: 0.0424 AC XY: 3155 AN XY: 74452

African (AFR) AF: 0.0427 AC: 1776 AN: 41568

American (AMR) AF: 0.0385 AC: 589 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5184

South Asian (SAS) AF: 0.0861 AC: 416 AN: 4830

European-Finnish (FIN) AF: 0.00868 AC: 92 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3090 AN: 67998

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0413 Hom.: 24

Bravo AF: 0.0454

Asia WGS AF: 0.0530 AC: 184 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.060
DANN	Benign	0.72
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs75316749; hg19: chr3-168761423;