rs2271489

chr3-39235168-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702477.1(ENSG00000287958):n.272+2366C>G variant causes a intron, non coding transcript 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: ENST00000702477.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724104	XR_940742.4	n.302+2366C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702477.1	n.272+2366C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.0943

Gnomad4 EAS AF: 0.0146

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0855

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0998

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.7
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2271489; hg19: chr3-39276659;