7-137345092-T-C

Variant summary

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

The ENST00000438969.2(ENSG00000228031):n.391A>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 0.566 in 152,122 control chromosomes in the GnomAD database, including 24,476 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 0.57 (24476 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENST00000438969.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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
	ENST00000438969.2	n.391A>G		non_coding_transcript_exon_variant	4/4	4

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86059 AN: 152004 Hom.: 24452 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.569

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.566 AC: 86119 AN: 152122 Hom.: 24476 Cov.: 33 AF XY: 0.567 AC XY: 42148 AN XY: 74376

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.570

Alfa AF: 0.570 Hom.: 5023

Bravo AF: 0.568

Asia WGS AF: 0.561 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.61
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs321198; hg19: chr7-137029838;