ENST00000799383.1:n.1673A>G

Variant names:

• chr2-155733297-T-C
• rs4664775
• ENST00000799383.1:n.1673A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000799383.1(ENSG00000304068):​n.1673A>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 0.963 in 152,238 control chromosomes in the GnomAD database, including 70,790 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 0.96 (70790 hom., cov: 31)
• Consequence: ENSG00000304068 ENST00000799383.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 0 publications found

Genes affected

ENSG00000304068 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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
ENSG00000304068	ENST00000799383.1	n.1673A>G		non_coding_transcript_exon_variant	Exon 9 of 9

Frequencies

GnomAD3 genomes AF: 0.963 AC: 146480 AN: 152120 Hom.: 70738 Cov.: 31

Gnomad AFR AF: 0.877

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.983

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.963 AC: 146589 AN: 152238 Hom.: 70790 Cov.: 31 AF XY: 0.965 AC XY: 71780 AN XY: 74416

African (AFR) AF: 0.877 AC: 36417 AN: 41514

American (AMR) AF: 0.984 AC: 15028 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3345 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5166

South Asian (SAS) AF: 0.999 AC: 4825 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10624 AN: 10626

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67956 AN: 68042

Other (OTH) AF: 0.965 AC: 2033 AN: 2106

Alfa AF: 0.978 Hom.: 3784

Bravo AF: 0.957

Asia WGS AF: 0.991 AC: 3448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4664775; hg19: chr2-156589809;