10-78380416-C-T

Variant names:

• chr10-78380416-C-T
• rs11002528
• ENST00000421324.4:n.50+142112C>T

Variant summary

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

The ENST00000421324.4(LINC00856):​n.50+142112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,314 control chromosomes in the GnomAD database, including 410 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 0.067 (410 hom., cov: 32)
  • Exomes 𝑓: 0.16 (0 hom.)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421324.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00856	ENST00000421324.4	TSL:1	n.50+142112C>T		intron	N/A
	LINC00856	ENST00000634452.1	TSL:2	n.169C>T		non_coding_transcript_exon	Exon 2 of 3
	LINC00856	ENST00000635545.1	TSL:4	n.335C>T		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10149 AN: 152134 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0858

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.0746

GnomAD4 exome AF: 0.161 AC: 10 AN: 62 Hom.: 0 Cov.: 0 AF XY: 0.109 AC XY: 5 AN XY: 46

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 8 AN: 48

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0667 AC: 10150 AN: 152252 Hom.: 410 Cov.: 32 AF XY: 0.0665 AC XY: 4950 AN XY: 74440

African (AFR) AF: 0.0164 AC: 681 AN: 41564

American (AMR) AF: 0.0671 AC: 1026 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3468

East Asian (EAS) AF: 0.0864 AC: 446 AN: 5160

South Asian (SAS) AF: 0.0521 AC: 251 AN: 4820

European-Finnish (FIN) AF: 0.0791 AC: 840 AN: 10614

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0939 AC: 6384 AN: 68018

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0294 Hom.: 23

Bravo AF: 0.0651

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.44
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11002528; hg19: chr10-80140173;