rs272000

chr2-115898219-G-C

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, non coding transcript 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: ENST00000668438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668438.1	n.361-2636C>G		intron_variant, non_coding_transcript_variant

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;