chr10-62656216-G-A

Position:

• chr10-62656216-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The XM_047426120.1(LOC124902436):​c.242-180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 152,276 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.029 (95 hom., cov: 32)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.157

Genes affected

LOC124902436 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 10-62656216-G-A is Benign according to our data. Variant chr10-62656216-G-A is described in ClinVar as [Benign]. Clinvar id is 1274565.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0288 (4390/152276) while in subpopulation NFE AF= 0.0402 (2737/68010). AF 95% confidence interval is 0.039. There are 95 homozygotes in gnomad4. There are 2171 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.242-180G>A		intron_variant			XP_047282076.1
LOC124902436	XM_047426118.1	c.398-180G>A		intron_variant			XP_047282074.1
LOC124902436	XM_047426119.1	c.398-180G>A		intron_variant			XP_047282075.1
LOC124902436	XM_047426121.1	c.548-180G>A		intron_variant			XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.726-180G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 4384 AN: 152158 Hom.: 94 Cov.: 32

Gnomad AFR AF: 0.00632

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0288 AC: 4390 AN: 152276 Hom.: 95 Cov.: 32 AF XY: 0.0292 AC XY: 2171 AN XY: 74452

Gnomad4 AFR AF: 0.00630

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.0402

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.0377 Hom.: 24

Bravo AF: 0.0243

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 24, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
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: rs117615414; hg19: chr10-64415976;