rs6546693

chr2-71453502-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000685766.2(ENSG00000289327):n.969A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,110 control chromosomes in the GnomAD database, including 2,867 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (2867 hom., cov: 32)
• Consequence: ENST00000685766.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.118

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 2-71453502-T-C is Benign according to our data. Variant chr2-71453502-T-C is described in ClinVar as [Benign]. Clinvar id is 679856.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685766.2	n.969A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24166 AN: 151992 Hom.: 2864 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.159 AC: 24196 AN: 152110 Hom.: 2867 Cov.: 32 AF XY: 0.163 AC XY: 12085 AN XY: 74368

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0767

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0991 Hom.: 1696

Bravo AF: 0.170

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	9.5
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6546693; hg19: chr2-71680632;