4-37043998-T-C

Variant names:

• chr4-37043998-T-C
• rs7655238
• ENST00000720070.1:n.123-34582T>C

Variant summary

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

The ENST00000720070.1(LINC02616):​n.123-34582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,874 control chromosomes in the GnomAD database, including 12,948 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 0.41 (12948 hom., cov: 32)
• Consequence: LINC02616 ENST00000720070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61
• Publications: 3 publications found

Genes affected

LINC02616 (HGNC:54078): (long intergenic non-protein coding RNA 2616)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 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
LINC02616	ENST00000720070.1	n.123-34582T>C		intron_variant	Intron 1 of 5
LINC02616	ENST00000720071.1	n.85-1739T>C		intron_variant	Intron 1 of 5
LINC02616	ENST00000720072.1	n.96-34582T>C		intron_variant	Intron 1 of 3
LINC02616	ENST00000720073.1	n.88-34472T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62339 AN: 151754 Hom.: 12942 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.411 AC: 62368 AN: 151874 Hom.: 12948 Cov.: 32 AF XY: 0.411 AC XY: 30486 AN XY: 74210

African (AFR) AF: 0.469 AC: 19399 AN: 41396

American (AMR) AF: 0.360 AC: 5500 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3466

East Asian (EAS) AF: 0.521 AC: 2684 AN: 5150

South Asian (SAS) AF: 0.399 AC: 1921 AN: 4816

European-Finnish (FIN) AF: 0.407 AC: 4290 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25700 AN: 67920

Other (OTH) AF: 0.395 AC: 836 AN: 2114

Alfa AF: 0.392 Hom.: 17036

Bravo AF: 0.409

Asia WGS AF: 0.471 AC: 1638 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.42
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs7655238; hg19: chr4-37045620;