3-169764347-G-A

Variant names:

• chr3-169764347-G-A
• rs35073794
• ENST00000738610.1:n.-39G>A

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The ENST00000738610.1(ENSG00000296372):​n.-39G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 152,322 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Genomes: 𝑓 0.014 (19 hom., cov: 32)
• Consequence: ENSG00000296372 ENST00000738610.1 upstream_gene
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.972
• Publications: 8 publications found

Genes affected

ENSG00000296372 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 3-169764347-G-A is Benign according to our data. Variant chr3-169764347-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1190126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd4 at 19 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296372	ENST00000738610.1	n.-39G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2131 AN: 152204 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.00661

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00500

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.00955

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

GnomAD4 genome AF: 0.0141 AC: 2155 AN: 152322 Hom.: 19 Cov.: 32 AF XY: 0.0135 AC XY: 1003 AN XY: 74486

African (AFR) AF: 0.0137 AC: 568 AN: 41582

American (AMR) AF: 0.00660 AC: 101 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3468

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5180

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4830

European-Finnish (FIN) AF: 0.00500 AC: 53 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1073 AN: 68024

Other (OTH) AF: 0.0156 AC: 33 AN: 2116

Alfa AF: 0.0176 Hom.: 3

Bravo AF: 0.0141

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 14, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs35073794; hg19: chr3-169482135;