rs2074136

chr7-118003214-T-C

Variant summary

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

The ENST00000427030.1(ENSG00000234826):n.106A>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 0.115 in 152,160 control chromosomes in the GnomAD database, including 2,577 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 0.12 (2577 hom., cov: 32)
  • Exomes 𝑓: 0.029 (0 hom.)
• Consequence: ENST00000427030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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
	ENST00000427030.1	n.106A>G		non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17490 AN: 151976 Hom.: 2571 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.100

GnomAD4 exome AF: 0.0294 AC: 2 AN: 68 Hom.: 0 Cov.: 0 AF XY: 0.0400 AC XY: 2 AN XY: 50

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0172

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.115 AC: 17514 AN: 152092 Hom.: 2577 Cov.: 32 AF XY: 0.114 AC XY: 8503 AN XY: 74372

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.0667

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.0672

Gnomad4 FIN AF: 0.00988

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0298 Hom.: 834

Bravo AF: 0.131

Asia WGS AF: 0.211 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.1
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2074136; hg19: chr7-117643268;