rs12768538

chr10-62646598-C-G

Variant summary

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

The XM_047426120.1(LOC124902436):c.38+2635C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,978 control chromosomes in the GnomAD database, including 7,949 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 (7949 hom., cov: 31)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902436	XM_047426120.1	c.38+2635C>G		intron_variant
LOC105378327	XR_946002.3	n.160+8828G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02929	ENST00000395251.5	n.372+2635C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44906 AN: 151862 Hom.: 7953 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.295 AC: 44889 AN: 151978 Hom.: 7949 Cov.: 31 AF XY: 0.297 AC XY: 22030 AN XY: 74260

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.292

Alfa AF: 0.312 Hom.: 999

Bravo AF: 0.275

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	1.3
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12768538; hg19: chr10-64406358;