rs12763437

Positions:

• chr10-78453560-G-A

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.51-75191G>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 0.0716 in 152,140 control chromosomes in the GnomAD database, including 446 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 0.072 (446 hom., cov: 32)
• Consequence: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984245	XR_001747513.2	n.3858+4360C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000421324.4	n.51-75191G>A		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-71770G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10889 AN: 152022 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0716 AC: 10892 AN: 152140 Hom.: 446 Cov.: 32 AF XY: 0.0696 AC XY: 5172 AN XY: 74360

Gnomad4 AFR AF: 0.0544

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.0754

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.0812

Alfa AF: 0.0725 Hom.: 58

Bravo AF: 0.0701

Asia WGS AF: 0.0530 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12763437; hg19: chr10-80213317;