3-169764347-G-A

Position:

• chr3-169764347-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

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: intergenic_region
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.972

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.169764347G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.00660

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.00500

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0156

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

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35073794; hg19: chr3-169482135;