rs2979687

Positions:

• chr8-24956889-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000607735.2(ENSG00000272157):​n.949T>C 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 0.625 in 322,422 control chromosomes in the GnomAD database, including 64,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.60 (27762 hom., cov: 29)
  • Exomes 𝑓: 0.65 (36338 hom.)
• Consequence: ENST00000607735.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -5.84

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 8-24956889-T-C is Benign according to our data. Variant chr8-24956889-T-C is described in ClinVar as [Benign]. Clinvar id is 667514.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.678 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
	ENST00000607735.2	n.949T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90182 AN: 151454 Hom.: 27741 Cov.: 29

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.585

GnomAD4 exome AF: 0.650 AC: 111127 AN: 170848 Hom.: 36338 Cov.: 0 AF XY: 0.651 AC XY: 58857 AN XY: 90408

Gnomad4 AFR exome AF: 0.421

Gnomad4 AMR exome AF: 0.715

Gnomad4 ASJ exome AF: 0.577

Gnomad4 EAS exome AF: 0.588

Gnomad4 SAS exome AF: 0.667

Gnomad4 FIN exome AF: 0.632

Gnomad4 NFE exome AF: 0.666

Gnomad4 OTH exome AF: 0.626

GnomAD4 genome AF: 0.595 AC: 90262 AN: 151574 Hom.: 27762 Cov.: 29 AF XY: 0.598 AC XY: 44262 AN XY: 74040

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.585

Alfa AF: 0.598 Hom.: 4544

Bravo AF: 0.594

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

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. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.057
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2979687; hg19: chr8-24814403;