3-35346652-C-T

Variant names:

• chr3-35346652-C-T
• rs1160578
• ENST00000797381.1:n.389-40128G>A

Variant summary

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

The ENST00000797381.1(ENSG00000289420):​n.389-40128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,372 control chromosomes in the GnomAD database, including 6,416 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 0.22 (6416 hom., cov: 32)
• Consequence: ENSG00000289420 ENST00000797381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 2 publications found

Genes affected

ENSG00000289420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797381.1. 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
	LOC101928135	NR_110817.1		n.153-40128G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289420	ENST00000797381.1		n.389-40128G>A		intron	N/A
	ENSG00000289420	ENST00000797382.1		n.389-40128G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32708 AN: 151254 Hom.: 6413 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.216 AC: 32741 AN: 151372 Hom.: 6416 Cov.: 32 AF XY: 0.211 AC XY: 15609 AN XY: 73960

African (AFR) AF: 0.525 AC: 21720 AN: 41342

American (AMR) AF: 0.125 AC: 1899 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 442 AN: 3456

East Asian (EAS) AF: 0.110 AC: 564 AN: 5122

South Asian (SAS) AF: 0.124 AC: 596 AN: 4822

European-Finnish (FIN) AF: 0.0595 AC: 630 AN: 10596

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6335 AN: 67576

Other (OTH) AF: 0.216 AC: 455 AN: 2102

Alfa AF: 0.0903 Hom.: 280

Bravo AF: 0.236

Asia WGS AF: 0.135 AC: 469 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.19
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1160578; hg19: chr3-35388144;