ENST00000762196.1:n.116T>G

Variant names:

• chr4-99404473-A-C
• rs1348276
• ENST00000762196.1:n.116T>G

Variant summary

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

The ENST00000762196.1(ENSG00000299279):​n.116T>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 0.458 in 151,934 control chromosomes in the GnomAD database, including 17,125 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 0.46 (17125 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 2 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762196.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299279	ENST00000762196.1		n.116T>G		non_coding_transcript_exon	Exon 1 of 5
	ENSG00000299279	ENST00000762194.1		n.154-295T>G		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.26-295T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69530 AN: 151816 Hom.: 17113 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.418

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69587 AN: 151934 Hom.: 17125 Cov.: 32 AF XY: 0.456 AC XY: 33873 AN XY: 74272

African (AFR) AF: 0.641 AC: 26563 AN: 41416

American (AMR) AF: 0.352 AC: 5369 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3150 AN: 5144

South Asian (SAS) AF: 0.502 AC: 2419 AN: 4822

European-Finnish (FIN) AF: 0.325 AC: 3433 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26272 AN: 67926

Other (OTH) AF: 0.419 AC: 883 AN: 2108

Alfa AF: 0.396 Hom.: 15927

Bravo AF: 0.468

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1348276; hg19: chr4-100325630;