rs300154

Variant names:

• chr2-17804719-A-G
• rs300154
• ENST00000750479.1:n.689T>C

Variant summary

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

The ENST00000750479.1(ENSG00000297720):​n.689T>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 0.552 in 152,092 control chromosomes in the GnomAD database, including 24,316 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 0.55 (24316 hom., cov: 33)
• Consequence: ENSG00000297720 ENST00000750479.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 4 publications found

Genes affected

ENSG00000297720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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
ENSG00000297720	ENST00000750479.1	n.689T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000297720	ENST00000750480.1	n.872T>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000297720	ENST00000750481.1	n.831T>C		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83875 AN: 151974 Hom.: 24302 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.552 AC: 83929 AN: 152092 Hom.: 24316 Cov.: 33 AF XY: 0.559 AC XY: 41568 AN XY: 74354

African (AFR) AF: 0.409 AC: 16976 AN: 41480

American (AMR) AF: 0.665 AC: 10172 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3468

East Asian (EAS) AF: 0.961 AC: 4982 AN: 5184

South Asian (SAS) AF: 0.798 AC: 3841 AN: 4814

European-Finnish (FIN) AF: 0.541 AC: 5711 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38296 AN: 67986

Other (OTH) AF: 0.568 AC: 1201 AN: 2114

Alfa AF: 0.520 Hom.: 8051

Bravo AF: 0.555

Asia WGS AF: 0.846 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.30
DANN	Benign	0.78
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs300154; hg19: chr2-17985986;