chr4-99385019-T-C

Variant names:

• chr4-99385019-T-C
• rs1442484
• ENST00000762375.1:n.726T>C

Variant summary

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

The ENST00000762375.1(ENSG00000299292):​n.726T>C 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 0.25 in 151,998 control chromosomes in the GnomAD database, including 5,546 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 0.25 (5546 hom., cov: 32)
• Consequence: ENSG00000299292 ENST00000762375.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 1 publications found

Genes affected

ENSG00000299292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762375.1. 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
	ENSG00000299292	ENST00000762375.1		n.726T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299279	ENST00000762194.1		n.378-1399A>G		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.250-1399A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37923 AN: 151880 Hom.: 5539 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.250 AC: 37957 AN: 151998 Hom.: 5546 Cov.: 32 AF XY: 0.257 AC XY: 19059 AN XY: 74280

African (AFR) AF: 0.307 AC: 12713 AN: 41466

American (AMR) AF: 0.182 AC: 2771 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3481 AN: 5160

South Asian (SAS) AF: 0.467 AC: 2245 AN: 4812

European-Finnish (FIN) AF: 0.173 AC: 1826 AN: 10580

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13524 AN: 67954

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.114 Hom.: 200

Bravo AF: 0.250

Asia WGS AF: 0.468 AC: 1625 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.87
DANN	Benign	0.84
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1442484; hg19: chr4-100306176;