rs6755560

chr2-206853059-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658889.1(ENSG00000229321):n.2974-26324T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,686 control chromosomes in the GnomAD database, including 5,559 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 0.26 (5559 hom., cov: 31)
• Consequence: ENST00000658889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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
	ENST00000658889.1	n.2974-26324T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39639 AN: 151568 Hom.: 5555 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.261 AC: 39656 AN: 151686 Hom.: 5559 Cov.: 31 AF XY: 0.259 AC XY: 19202 AN XY: 74102

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0295

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.266

Alfa AF: 0.284 Hom.: 1450

Bravo AF: 0.258

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6755560; hg19: chr2-207717783;