2-215727165-A-G

Position:

• chr2-215727165-A-G

Variant summary

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

The ENST00000423530.5(LINC00607):​n.476+16649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,086 control chromosomes in the GnomAD database, including 23,321 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 0.49 (23321 hom., cov: 32)
• Consequence: LINC00607 ENST00000423530.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

LINC00607 (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 (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00607	NR_037195.1	n.723+13712T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00607	ENST00000417922.2	n.510+16649T>C		intron_variant		4
LINC00607	ENST00000423530.5	n.476+16649T>C		intron_variant		2
LINC00607	ENST00000445174.5	n.723+13712T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74838 AN: 151964 Hom.: 23330 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.492 AC: 74811 AN: 152086 Hom.: 23321 Cov.: 32 AF XY: 0.487 AC XY: 36234 AN XY: 74376

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.522

Alfa AF: 0.597 Hom.: 3783

Bravo AF: 0.457

Asia WGS AF: 0.159 AC: 556 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	3.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10202705; hg19: chr2-216591888;