4-99067508-C-T

Variant names:

• chr4-99067508-C-T
• rs1230154
• ENST00000609071.1:n.618G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000272777 ENST00000609071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 8 publications found

Genes affected

ENSG00000272777 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272777	ENST00000609071.1	n.618G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.762 AC: 115884 AN: 152046 Hom.: 44535 Cov.: 31 AF XY: 0.770 AC XY: 57196 AN XY: 74312

African (AFR) AF: 0.826 AC: 34289 AN: 41494

American (AMR) AF: 0.756 AC: 11553 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5151 AN: 5184

South Asian (SAS) AF: 0.863 AC: 4159 AN: 4820

European-Finnish (FIN) AF: 0.741 AC: 7800 AN: 10532

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48209 AN: 67954

Other (OTH) AF: 0.737 AC: 1555 AN: 2110

Alfa AF: 0.721 Hom.: 38872

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
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs1230154; hg19: chr4-99988659;