rs272000

Variant names:

• chr2-115898219-G-C
• rs272000
• ENST00000668438.1:n.361-2636C>G

Variant summary

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

The ENST00000668438.1(ENSG00000287451):​n.361-2636C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,946 control chromosomes in the GnomAD database, including 23,661 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 0.54 (23661 hom., cov: 32)
• Consequence: ENSG00000287451 ENST00000668438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

Genes affected

ENSG00000287451 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 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
ENSG00000287451	ENST00000668438.1	n.361-2636C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82480 AN: 151828 Hom.: 23653 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.543 AC: 82517 AN: 151946 Hom.: 23661 Cov.: 32 AF XY: 0.545 AC XY: 40429 AN XY: 74246

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.567

Alfa AF: 0.568 Hom.: 3134

Bravo AF: 0.539

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs272000; hg19: chr2-116655795;