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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791974.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303122	ENST00000791974.1		n.363-11827T>C		intron	N/A
	ENSG00000303122	ENST00000791976.1		n.157+6083T>C		intron	N/A
	ENSG00000303137	ENST00000792140.1		n.107+1488A>G		intron	N/A

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 v4.9

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;