chr10-78427948-G-A

Position:

• chr10-78427948-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421324.4(ENSG00000282863):​n.51-100803G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,156 control chromosomes in the GnomAD database, including 1,010 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 0.099 (1010 hom., cov: 32)
• Consequence: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000421324.4	n.51-100803G>A		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-97382G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15140 AN: 152038 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0995 AC: 15139 AN: 152156 Hom.: 1010 Cov.: 32 AF XY: 0.0971 AC XY: 7219 AN XY: 74372

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0897

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.107

Alfa AF: 0.124 Hom.: 759

Bravo AF: 0.100

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11812623; hg19: chr10-80187705;