rs1916400

Positions:

• chr10-78331581-T-C

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.50+93277T>C 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 0.297 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: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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.50+93277T>C		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.62+152335T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.283

Alfa AF: 0.199 Hom.: 1974

Bravo AF: 0.318

Asia WGS AF: 0.393 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1916400; hg19: chr10-80091338;