rs2271489

Variant names:

• chr3-39235168-C-G
• rs2271489
• ENST00000702477.2:n.302+2366C>G

Variant summary

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

The ENST00000702477.2(ENSG00000287958):​n.302+2366C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 152,274 control chromosomes in the GnomAD database, including 743 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 0.093 (743 hom., cov: 31)
• Consequence: ENSG00000287958 ENST00000702477.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 2 publications found

Genes affected

ENSG00000287958 (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 (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702477.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287958	ENST00000702477.2		n.302+2366C>G		intron	N/A
	ENSG00000287958	ENST00000785475.1		n.96+7406C>G		intron	N/A
	ENSG00000287958	ENST00000785476.1		n.56-3918C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14177 AN: 152154 Hom.: 742 Cov.: 31

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0847

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0931 AC: 14184 AN: 152274 Hom.: 743 Cov.: 31 AF XY: 0.0917 AC XY: 6828 AN XY: 74446

African (AFR) AF: 0.0785 AC: 3261 AN: 41556

American (AMR) AF: 0.0845 AC: 1293 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0943 AC: 327 AN: 3468

East Asian (EAS) AF: 0.0146 AC: 76 AN: 5188

South Asian (SAS) AF: 0.103 AC: 495 AN: 4826

European-Finnish (FIN) AF: 0.0855 AC: 906 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7454 AN: 68020

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0947 Hom.: 94

Bravo AF: 0.0920

Asia WGS AF: 0.0510 AC: 179 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	6.7
DANN	Benign	0.67
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2271489; hg19: chr3-39276659;