rs1916400

Variant names:

• chr10-78331581-T-C
• rs1916400
• ENST00000421324.4:n.50+93277T>C

Variant summary

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

The ENST00000421324.4(LINC00856):​n.50+93277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,734 control chromosomes in the GnomAD database, including 8,947 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 0.30 (8947 hom., cov: 31)
• Consequence: LINC00856 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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+93277T>C		intron	N/A
	LINC00856	ENST00000432742.1	TSL:3	n.439-21511T>C		intron	N/A
	LINC00856	ENST00000624665.3	TSL:2	n.331+82511T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45005 AN: 151616 Hom.: 8926 Cov.: 31

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.297 AC: 45077 AN: 151734 Hom.: 8947 Cov.: 31 AF XY: 0.297 AC XY: 22043 AN XY: 74156

African (AFR) AF: 0.556 AC: 22959 AN: 41324

American (AMR) AF: 0.267 AC: 4077 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2486 AN: 5120

South Asian (SAS) AF: 0.278 AC: 1332 AN: 4794

European-Finnish (FIN) AF: 0.145 AC: 1530 AN: 10558

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11167 AN: 67904

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.215 Hom.: 3366

Bravo AF: 0.318

Asia WGS AF: 0.393 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.8
DANN	Benign	0.65
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs1916400; hg19: chr10-80091338;