10-62655424-A-G

Variant summary

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

The XM_047426120.1(LOC124902436):c.184A>G(p.Thr62Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,613,968 control chromosomes in the GnomAD database, including 475,776 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict 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 (50907 hom., cov: 31)
  • Exomes 𝑓: 0.76 (424869 hom.)
• Consequence: LOC124902436 XM_047426120.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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 (MetaRNN=6.7336487E-7).
• 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	UniProt
LOC124902436	XM_047426120.1	c.184A>G	p.Thr62Ala	missense_variant	3/6
LOC105378327	XR_946002.3	n.160+2T>C		splice_donor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02929	ENST00000395251.5	n.518A>G		non_coding_transcript_exon_variant	4/7	1

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123385 AN: 151986 Hom.: 50848 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.785

GnomAD3 exomes AF: 0.797 AC: 200272 AN: 251422 Hom.: 80675 AF XY: 0.791 AC XY: 107479 AN XY: 135886

Gnomad AFR exome AF: 0.954

Gnomad AMR exome AF: 0.871

Gnomad ASJ exome AF: 0.720

Gnomad EAS exome AF: 0.909

Gnomad SAS exome AF: 0.867

Gnomad FIN exome AF: 0.751

Gnomad NFE exome AF: 0.732

Gnomad OTH exome AF: 0.763

GnomAD4 exome AF: 0.760 AC: 1110768 AN: 1461864 Hom.: 424869 Cov.: 68 AF XY: 0.761 AC XY: 553436 AN XY: 727232

Gnomad4 AFR exome AF: 0.954

Gnomad4 AMR exome AF: 0.864

Gnomad4 ASJ exome AF: 0.716

Gnomad4 EAS exome AF: 0.924

Gnomad4 SAS exome AF: 0.864

Gnomad4 FIN exome AF: 0.749

Gnomad4 NFE exome AF: 0.737

Gnomad4 OTH exome AF: 0.770

GnomAD4 genome AF: 0.812 AC: 123501 AN: 152104 Hom.: 50907 Cov.: 31 AF XY: 0.813 AC XY: 60465 AN XY: 74362

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.782

Alfa AF: 0.749 Hom.: 109719

Bravo AF: 0.824

TwinsUK AF: 0.746 AC: 2768

ALSPAC AF: 0.740 AC: 2852

ESP6500AA AF: 0.946 AC: 4167

ESP6500EA AF: 0.734 AC: 6311

ExAC AF: 0.794 AC: 96363

Asia WGS AF: 0.867 AC: 3016 AN: 3478

EpiCase AF: 0.733

EpiControl AF: 0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.79	T
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.034
Dann	Benign	0.48
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.0024	N
LIST_S2	Benign	0.11	T
MetaRNN	Benign	6.7e-7	T
MetaSVM	Benign	-0.99	T
MutationTaster	Benign	1.0	P;P;P
Sift4G	Benign	0.91	T
Vest4		0.0050
ClinPred		0.0013	T
GERP RS		-6.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7076156; hg19: chr10-64415184;