chr1-72371556-T-C

Variant names:

• chr1-72371556-T-C
• rs7531118
• ENST00000715640.2:n.236+88151T>C

Variant summary

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

The ENST00000715640.2(LINC02796):​n.236+88151T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,118 control chromosomes in the GnomAD database, including 15,213 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 0.40 (15213 hom., cov: 32)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 60 publications found

Genes affected

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

LOC105378797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.472+88151T>C		intron_variant	Intron 1 of 7
LOC105378797	XR_001737671.3	n.472+88151T>C		intron_variant	Intron 1 of 5
LOC105378797	XR_947505.3	n.472+88151T>C		intron_variant	Intron 1 of 6
LOC105378797	XR_947506.3	n.472+88151T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02796	ENST00000715640.2	n.236+88151T>C		intron_variant	Intron 1 of 6
LINC02796	ENST00000715641.1	n.227+88151T>C		intron_variant	Intron 1 of 2
LINC02796	ENST00000715642.1	n.153+88151T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61089 AN: 152000 Hom.: 15214 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.402 AC: 61095 AN: 152118 Hom.: 15213 Cov.: 32 AF XY: 0.404 AC XY: 30029 AN XY: 74350

African (AFR) AF: 0.112 AC: 4647 AN: 41548

American (AMR) AF: 0.436 AC: 6651 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1396 AN: 5154

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6276 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37053 AN: 67976

Other (OTH) AF: 0.424 AC: 892 AN: 2104

Alfa AF: 0.491 Hom.: 64684

Bravo AF: 0.380

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.7
DANN	Benign	0.89
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7531118; hg19: chr1-72837239;