ENST00000612706.2:n.1111T>G

Variant names:

• chr4-89685367-T-G
• rs3857047
• ENST00000612706.2:n.1111T>G

Variant summary

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

The ENST00000612706.2(ENSG00000251095):​n.1111T>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 0.21 in 152,152 control chromosomes in the GnomAD database, including 4,737 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 0.21 (4737 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000251095 ENST00000612706.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612706.2. 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.1111T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000251095	ENST00000506864.5	TSL:4	n.472-5918T>G		intron	N/A
	ENSG00000251095	ENST00000507916.6	TSL:3	n.135-5918T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31967 AN: 152034 Hom.: 4727 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.176

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.210 AC: 31994 AN: 152152 Hom.: 4737 Cov.: 32 AF XY: 0.205 AC XY: 15215 AN XY: 74382

African (AFR) AF: 0.417 AC: 17296 AN: 41468

American (AMR) AF: 0.139 AC: 2122 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0679 AC: 328 AN: 4830

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9829 AN: 68008

Other (OTH) AF: 0.174 AC: 367 AN: 2112

Alfa AF: 0.156 Hom.: 4563

Bravo AF: 0.219

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.55
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3857047;

hg19: chr4-90606518;