chr3-147379060-C-A

Variant names:

• chr3-147379060-C-A
• rs1394041
• ENST00000770125.1:n.85-2132G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000770125.1(ENSG00000300216):​n.85-2132G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,132 control chromosomes in the GnomAD database, including 843 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 0.096 (843 hom., cov: 33)
• Consequence: ENSG00000300216 ENST00000770125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 7 publications found

Genes affected

ENSG00000300216 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770125.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300216	ENST00000770125.1		n.85-2132G>T		intron	N/A
	ENSG00000300216	ENST00000770126.1		n.130-2132G>T		intron	N/A
	ENSG00000300216	ENST00000770127.1		n.67-2132G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0963 AC: 14636 AN: 152014 Hom.: 844 Cov.: 33

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0962 AC: 14641 AN: 152132 Hom.: 843 Cov.: 33 AF XY: 0.0984 AC XY: 7319 AN XY: 74350

African (AFR) AF: 0.0322 AC: 1338 AN: 41536

American (AMR) AF: 0.0852 AC: 1303 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3466

East Asian (EAS) AF: 0.163 AC: 840 AN: 5152

South Asian (SAS) AF: 0.125 AC: 599 AN: 4810

European-Finnish (FIN) AF: 0.174 AC: 1834 AN: 10552

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8099 AN: 68012

Other (OTH) AF: 0.0868 AC: 183 AN: 2108

Alfa AF: 0.108 Hom.: 1624

Bravo AF: 0.0869

Asia WGS AF: 0.132 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	22
DANN	Benign	0.83
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1394041; hg19: chr3-147096847;