1-72548334-G-C

Variant names:

• chr1-72548334-G-C
• rs1418624
• ENST00000715640.2:n.397-6877G>C

Variant summary

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

The ENST00000715640.2(LINC02796):​n.397-6877G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 151,932 control chromosomes in the GnomAD database, including 68,216 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 0.95 (68216 hom., cov: 32)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715640.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02796	ENST00000715640.2		n.397-6877G>C		intron	N/A
	LINC02796	ENST00000715642.1		n.202-6877G>C		intron	N/A
	LINC02796	ENST00000715643.1		n.217-6877G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143581 AN: 151814 Hom.: 68169 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.946 AC: 143685 AN: 151932 Hom.: 68216 Cov.: 32 AF XY: 0.948 AC XY: 70389 AN XY: 74278

African (AFR) AF: 0.855 AC: 35511 AN: 41526

American (AMR) AF: 0.946 AC: 14376 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3436 AN: 3464

East Asian (EAS) AF: 0.951 AC: 4921 AN: 5176

South Asian (SAS) AF: 0.991 AC: 4780 AN: 4822

European-Finnish (FIN) AF: 0.995 AC: 10550 AN: 10608

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 66887 AN: 67826

Other (OTH) AF: 0.960 AC: 2022 AN: 2106

Alfa AF: 0.962 Hom.: 8216

Bravo AF: 0.939

Asia WGS AF: 0.973 AC: 3381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1418624; hg19: chr1-73014017;