chr1-72346221-G-T

Variant names:

• chr1-72346221-G-T
• rs11209948
• ENST00000715640.2:n.236+62816G>T

Variant summary

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

The ENST00000715640.2(LINC02796):​n.236+62816G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,856 control chromosomes in the GnomAD database, including 31,342 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 0.64 (31342 hom., cov: 31)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 27 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.472+62816G>T		intron_variant	Intron 1 of 7
LOC105378797	XR_001737671.3	n.472+62816G>T		intron_variant	Intron 1 of 5
LOC105378797	XR_947505.3	n.472+62816G>T		intron_variant	Intron 1 of 6
LOC105378797	XR_947506.3	n.472+62816G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02796	ENST00000715640.2	n.236+62816G>T		intron_variant	Intron 1 of 6
LINC02796	ENST00000715641.1	n.227+62816G>T		intron_variant	Intron 1 of 2
LINC02796	ENST00000715642.1	n.153+62816G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96702 AN: 151738 Hom.: 31325 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.637 AC: 96757 AN: 151856 Hom.: 31342 Cov.: 31 AF XY: 0.643 AC XY: 47730 AN XY: 74224

African (AFR) AF: 0.584 AC: 24168 AN: 41414

American (AMR) AF: 0.711 AC: 10848 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2549 AN: 3464

East Asian (EAS) AF: 0.923 AC: 4751 AN: 5148

South Asian (SAS) AF: 0.668 AC: 3214 AN: 4812

European-Finnish (FIN) AF: 0.649 AC: 6852 AN: 10564

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42279 AN: 67888

Other (OTH) AF: 0.653 AC: 1375 AN: 2106

Alfa AF: 0.586 Hom.: 5721

Bravo AF: 0.642

Asia WGS AF: 0.758 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.49
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11209948; hg19: chr1-72811904;