chr10-62654300-G-A

Position:

• chr10-62654300-G-A

Variant summary

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

The XM_047426120.1(LOC124902436):​c.39-543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,134 control chromosomes in the GnomAD database, including 50,928 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 0.81 (50928 hom., cov: 31)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

LOC124902436 (HGNC:):

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.39-543G>A		intron_variant			XP_047282076.1
LOC105378327	XR_946002.3	n.160+1126C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.373-543G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123424 AN: 152016 Hom.: 50869 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.812 AC: 123540 AN: 152134 Hom.: 50928 Cov.: 31 AF XY: 0.813 AC XY: 60463 AN XY: 74354

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.783

Alfa AF: 0.775 Hom.: 7836

Bravo AF: 0.824

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071642; hg19: chr10-64414060;