chr10-78267509-G-A

Variant names:

• chr10-78267509-G-A
• rs1720293
• ENST00000421324.4:n.50+29205G>A

Variant summary

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

The ENST00000421324.4(LINC00856):​n.50+29205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,008 control chromosomes in the GnomAD database, including 8,511 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 0.32 (8508 hom., cov: 33)
  • Exomes 𝑓: 0.39 (3 hom.)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 1 publications found

Genes affected

LINC00856 (HGNC:45111): (long intergenic non-protein coding RNA 856)

LINC00595 (HGNC:31430): (long intergenic non-protein coding RNA 595)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00595	NR_073447.2	n.145+23G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00856	ENST00000421324.4	n.50+29205G>A		intron_variant	Intron 1 of 2	1
LINC00856	ENST00000415959.1	n.159+23G>A		intron_variant	Intron 1 of 2	3
LINC00856	ENST00000432742.1	n.438+17058G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48451 AN: 151856 Hom.: 8503 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.389 AC: 14 AN: 36 Hom.: 3 Cov.: 0 AF XY: 0.412 AC XY: 14 AN XY: 34

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.462 AC: 12 AN: 26

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.319 AC: 48483 AN: 151972 Hom.: 8508 Cov.: 33 AF XY: 0.330 AC XY: 24481 AN XY: 74254

African (AFR) AF: 0.201 AC: 8338 AN: 41476

American (AMR) AF: 0.328 AC: 5019 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3525 AN: 5154

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4812

European-Finnish (FIN) AF: 0.471 AC: 4967 AN: 10536

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22496 AN: 67914

Other (OTH) AF: 0.296 AC: 625 AN: 2112

Alfa AF: 0.318 Hom.: 9531

Bravo AF: 0.303

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1720293; hg19: chr10-80027266;