2-215712980-G-A

Position:

• chr2-215712980-G-A

Variant summary

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

The ENST00000423530.5(LINC00607):​n.476+30834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,922 control chromosomes in the GnomAD database, including 24,809 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 0.53 (24809 hom., cov: 31)
• Consequence: LINC00607 ENST00000423530.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

Genes affected

ENSG00000237525 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00607	NR_037195.1	n.723+27897C>T		intron_variant
LOC102724861	NR_187736.1	n.623-260G>A		intron_variant
LOC102724861	NR_187737.1	n.1005-260G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000237525	ENST00000417485.6	n.987-260G>A		intron_variant		5
LINC00607	ENST00000417922.2	n.511-11761C>T		intron_variant		4
LINC00607	ENST00000423530.5	n.476+30834C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80953 AN: 151806 Hom.: 24816 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.533 AC: 80940 AN: 151922 Hom.: 24809 Cov.: 31 AF XY: 0.528 AC XY: 39208 AN XY: 74224

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.0503

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.551

Alfa AF: 0.659 Hom.: 44173

Bravo AF: 0.500

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498043; hg19: chr2-216577703;