2-215766643-C-T

Variant names:

• chr2-215766643-C-T
• rs4674024
• ENST00000413563.6:n.17-16226G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413563.6(LINC00607):​n.17-16226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,980 control chromosomes in the GnomAD database, including 14,805 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 0.44 (14805 hom., cov: 33)
• Consequence: LINC00607 ENST00000413563.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 5 publications found

Genes affected

LINC00607 (HGNC:43944): (long intergenic non-protein coding RNA 607)

ENSG00000288791 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00607	NR_037195.1	n.212-16226G>A		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00607	ENST00000413563.6	n.17-16226G>A		intron_variant	Intron 1 of 3	4
LINC00607	ENST00000417922.2	n.144-16226G>A		intron_variant	Intron 1 of 5	4
LINC00607	ENST00000423530.5	n.285-19249G>A		intron_variant	Intron 2 of 8	2

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66632 AN: 151860 Hom.: 14806 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.439 AC: 66676 AN: 151980 Hom.: 14805 Cov.: 33 AF XY: 0.439 AC XY: 32606 AN XY: 74296

African (AFR) AF: 0.386 AC: 15999 AN: 41438

American (AMR) AF: 0.541 AC: 8266 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2299 AN: 5152

South Asian (SAS) AF: 0.349 AC: 1678 AN: 4814

European-Finnish (FIN) AF: 0.447 AC: 4704 AN: 10528

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30749 AN: 67968

Other (OTH) AF: 0.420 AC: 887 AN: 2114

Alfa AF: 0.446 Hom.: 66857

Bravo AF: 0.440

Asia WGS AF: 0.427 AC: 1487 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.37
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4674024; hg19: chr2-216631366;