3-35346896-A-G

Variant names:

• chr3-35346896-A-G
• rs7631209
• ENST00000797381.1:n.389-40372T>C

Variant summary

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

The ENST00000797381.1(ENSG00000289420):​n.389-40372T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 151,350 control chromosomes in the GnomAD database, including 1,867 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 0.13 (1867 hom., cov: 32)
• Consequence: ENSG00000289420 ENST00000797381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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.153-40372T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289420	ENST00000797381.1		n.389-40372T>C		intron	N/A
	ENSG00000289420	ENST00000797382.1		n.389-40372T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20054 AN: 151232 Hom.: 1870 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.133 AC: 20072 AN: 151350 Hom.: 1867 Cov.: 32 AF XY: 0.128 AC XY: 9488 AN XY: 73980

African (AFR) AF: 0.259 AC: 10725 AN: 41352

American (AMR) AF: 0.0947 AC: 1435 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 348 AN: 3452

East Asian (EAS) AF: 0.109 AC: 555 AN: 5082

South Asian (SAS) AF: 0.108 AC: 521 AN: 4822

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10604

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.0840 AC: 5677 AN: 67582

Other (OTH) AF: 0.149 AC: 313 AN: 2098

Alfa AF: 0.110 Hom.: 226

Bravo AF: 0.144

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7631209; hg19: chr3-35388388;