chr10-78341104-T-C

Variant names:

• chr10-78341104-T-C
• rs2395528
• ENST00000421324.4:n.50+102800T>C

Variant summary

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

The ENST00000421324.4(LINC00595):​n.50+102800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 148,914 control chromosomes in the GnomAD database, including 44,493 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 0.77 (44493 hom., cov: 26)
• Consequence: LINC00595 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 5 publications found

Genes affected

LINC00595 (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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.796 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

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
	LINC00595	ENST00000421324.4	TSL:1	n.50+102800T>C		intron	N/A
	LINC00595	ENST00000432742.1	TSL:3	n.439-11988T>C		intron	N/A
	LINC00595	ENST00000624665.3	TSL:2	n.331+92034T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.772 AC: 114868 AN: 148872 Hom.: 44470 Cov.: 26

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.772 AC: 114912 AN: 148914 Hom.: 44493 Cov.: 26 AF XY: 0.768 AC XY: 55766 AN XY: 72590

African (AFR) AF: 0.778 AC: 31522 AN: 40518

American (AMR) AF: 0.808 AC: 12111 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2945 AN: 3466

East Asian (EAS) AF: 0.729 AC: 3731 AN: 5120

South Asian (SAS) AF: 0.767 AC: 3609 AN: 4706

European-Finnish (FIN) AF: 0.673 AC: 6348 AN: 9430

Middle Eastern (MID) AF: 0.775 AC: 220 AN: 284

European-Non Finnish (NFE) AF: 0.772 AC: 52033 AN: 67420

Other (OTH) AF: 0.797 AC: 1651 AN: 2072

Alfa AF: 0.775 Hom.: 130082

Bravo AF: 0.784

Asia WGS AF: 0.730 AC: 2539 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2395528; hg19: chr10-80100861;