4-99067508-C-T

Position:

• chr4-99067508-C-T

Variant summary

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

The ENST00000609071.1(ENSG00000272777):​n.618G>A 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 0.762 in 152,046 control chromosomes in the GnomAD database, including 44,535 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 0.76 (44535 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENST00000609071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000609071.1	n.618G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115796 AN: 151930 Hom.: 44503 Cov.: 31

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.734

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: 0.762 AC: 115884 AN: 152046 Hom.: 44535 Cov.: 31 AF XY: 0.770 AC XY: 57196 AN XY: 74312

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.737

Alfa AF: 0.719 Hom.: 33524

Bravo AF: 0.764

Asia WGS AF: 0.909 AC: 3157 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.94
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1230154; hg19: chr4-99988659;