4-89685446-C-T

Variant names:

• chr4-89685446-C-T
• rs356229
• ENST00000612706.2:n.1190C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659714.1(ENSG00000251095):​n.700C>T 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 0.687 in 151,994 control chromosomes in the GnomAD database, including 36,316 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 0.69 (36314 hom., cov: 31)
  • Exomes 𝑓: 0.58 (2 hom.)
• Consequence: ENSG00000251095 ENST00000659714.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 25 publications found

Genes affected

ENSG00000251095 (HGNC:53614):

LOC124900602 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659714.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251095	ENST00000612706.2	TSL:5	n.1190C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000251095	ENST00000659714.1		n.700C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000251095	ENST00000776711.1		n.214C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104399 AN: 151864 Hom.: 36303 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.662

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

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) AF: 0.583 AC: 7 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.687 AC: 104452 AN: 151982 Hom.: 36314 Cov.: 31 AF XY: 0.691 AC XY: 51316 AN XY: 74246

African (AFR) AF: 0.704 AC: 29174 AN: 41440

American (AMR) AF: 0.743 AC: 11353 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5064 AN: 5150

South Asian (SAS) AF: 0.782 AC: 3762 AN: 4810

European-Finnish (FIN) AF: 0.677 AC: 7136 AN: 10534

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43534 AN: 67980

Other (OTH) AF: 0.665 AC: 1404 AN: 2110

Alfa AF: 0.660 Hom.: 66710

Bravo AF: 0.692

Asia WGS AF: 0.859 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		0.098
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs356229; hg19: chr4-90606597;