chr10-2501620-C-T

Variant names:

• chr10-2501620-C-T
• rs568827865
• XM_011519770.3:c.328G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The XM_011519770.3(LOC107983989):​c.328G>A​(p.Val110Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00661 in 146,682 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0066 (15 hom., cov: 27)
• Consequence: LOC107983989 XM_011519770.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.117

Genes affected

LOC107983989 (HGNC:):

LINC02645 (HGNC:54129): (long intergenic non-protein coding RNA 2645)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 10-2501620-C-T is Benign according to our data. Variant chr10-2501620-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640278.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983989	XM_011519770.3	c.328G>A	p.Val110Met	missense_variant	Exon 1 of 2		XP_011518072.1
LINC02645	NR_136146.1	n.-158G>A		upstream_gene_variant
LOC105376350	NR_188171.1	n.-233C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02645	ENST00000414107.6	n.96G>A		non_coding_transcript_exon_variant	Exon 2 of 4	3
LINC02645	ENST00000662131.1	n.150G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000235281	ENST00000664280.1	n.21C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.00662 AC: 970 AN: 146586 Hom.: 15 Cov.: 27

Gnomad AFR AF: 0.00243

Gnomad AMI AF: 0.0565

Gnomad AMR AF: 0.00692

Gnomad ASJ AF: 0.00321

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00150

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00903

Gnomad OTH AF: 0.00496

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

GnomAD4 genome AF: 0.00661 AC: 970 AN: 146682 Hom.: 15 Cov.: 27 AF XY: 0.00658 AC XY: 471 AN XY: 71606

Gnomad4 AFR AF: 0.00242

Gnomad4 AMR AF: 0.00692

Gnomad4 ASJ AF: 0.00321

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00150

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.00903

Gnomad4 OTH AF: 0.00491

Alfa AF: 0.0163 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ENSG00000235281: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs568827865; hg19: chr10-2543812;