rs4571015

Variant names:

• chr2-154689158-G-T
• rs4571015
• ENST00000654516.1:n.3092C>A

Variant summary

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

The ENST00000654516.1(ENSG00000287900):​n.3092C>A 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 0.124 in 152,088 control chromosomes in the GnomAD database, including 1,322 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 0.12 (1322 hom., cov: 32)
• Consequence: ENSG00000287900 ENST00000654516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 3 publications found

Genes affected

ENSG00000287900 (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 (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654516.1. 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
	ENSG00000287900	ENST00000654516.1		n.3092C>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000287900	ENST00000662205.1		n.*234C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18891 AN: 151970 Hom.: 1313 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.124 AC: 18932 AN: 152088 Hom.: 1322 Cov.: 32 AF XY: 0.123 AC XY: 9179 AN XY: 74348

African (AFR) AF: 0.181 AC: 7485 AN: 41450

American (AMR) AF: 0.0860 AC: 1315 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3470

East Asian (EAS) AF: 0.185 AC: 957 AN: 5176

South Asian (SAS) AF: 0.119 AC: 575 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1212 AN: 10600

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0979 AC: 6654 AN: 67970

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.102 Hom.: 958

Bravo AF: 0.123

Asia WGS AF: 0.160 AC: 558 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	2.1
DANN	Benign	0.44
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4571015; hg19: chr2-155545670;