rs6542427

chr2-118044105-C-A

Variant summary

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

The ENST00000627670.3(ENSG00000235066):n.1227-10590C>A 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 0.279 in 151,888 control chromosomes in the GnomAD database, including 6,300 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 0.28 (6300 hom., cov: 32)
• Consequence: ENST00000627670.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 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
	ENST00000627670.3	n.1227-10590C>A		intron_variant, non_coding_transcript_variant		5
	ENST00000627626.1	n.247-10615C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42333 AN: 151770 Hom.: 6289 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.279 AC: 42367 AN: 151888 Hom.: 6300 Cov.: 32 AF XY: 0.276 AC XY: 20492 AN XY: 74242

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.267

Alfa AF: 0.274 Hom.: 2853

Bravo AF: 0.284

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.91
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6542427; hg19: chr2-118801681;