rs6429432

Variant names:

• chr1-235943941-A-C
• rs6429432
• ENST00000715678.1:n.206-912T>G

Variant summary

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

The ENST00000715678.1(LINC02768):​n.206-912T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,480 control chromosomes in the GnomAD database, including 65,926 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 0.93 (65842 hom., cov: 31)
  • Exomes 𝑓: 0.85 (84 hom.)
• Consequence: LINC02768 ENST00000715678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 5 publications found

Genes affected

LINC02768 (HGNC:54288): (long intergenic non-protein coding RNA 2768)

ENSG00000302457 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02768	NR_183724.1	n.873+13941T>G		intron_variant	Intron 2 of 2
LOC105373215	XR_001738537.2	n.520-10932A>C		intron_variant	Intron 2 of 2
LOC105373215	XR_001738539.2	n.520-10932A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02768	ENST00000715678.1	n.206-912T>G		intron_variant	Intron 2 of 2
ENSG00000302457	ENST00000786952.1	n.210-18380A>C		intron_variant	Intron 1 of 1
ENSG00000302457	ENST00000786953.1	n.224-10932A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141337 AN: 152126 Hom.: 65781 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.920

GnomAD4 exome AF: 0.847 AC: 200 AN: 236 Hom.: 84 AF XY: 0.819 AC XY: 131 AN XY: 160

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.837 AC: 87 AN: 104

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.856 AC: 101 AN: 118

Other (OTH) AF: 0.875 AC: 7 AN: 8

GnomAD4 genome AF: 0.929 AC: 141458 AN: 152244 Hom.: 65842 Cov.: 31 AF XY: 0.931 AC XY: 69312 AN XY: 74426

African (AFR) AF: 0.975 AC: 40488 AN: 41546

American (AMR) AF: 0.944 AC: 14447 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3000 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5180

South Asian (SAS) AF: 0.968 AC: 4659 AN: 4812

European-Finnish (FIN) AF: 0.922 AC: 9771 AN: 10594

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60851 AN: 68020

Other (OTH) AF: 0.921 AC: 1948 AN: 2114

Alfa AF: 0.921 Hom.: 20841

Bravo AF: 0.931

Asia WGS AF: 0.982 AC: 3414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6429432; hg19: chr1-236107241;