10-20610679-T-C

Variant summary

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

The XR_007062080.1(LOC105376442):n.1247T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,960 control chromosomes in the GnomAD database, including 7,621 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 0.31 (7621 hom., cov: 32)
• Consequence: LOC105376442 XR_007062080.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

LOC105376442 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376442	XR_007062080.1	n.1247T>C		non_coding_transcript_exon_variant	4/4
LOC105376442	XR_007062081.1	n.1351T>C		non_coding_transcript_exon_variant	4/4
LOC105376442	XR_930729.3	n.1396T>C		non_coding_transcript_exon_variant	4/4
LOC105376442	XR_930733.3	n.1442T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46343 AN: 151842 Hom.: 7624 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.305 AC: 46354 AN: 151960 Hom.: 7621 Cov.: 32 AF XY: 0.294 AC XY: 21862 AN XY: 74248

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.332

Alfa AF: 0.348 Hom.: 21097

Bravo AF: 0.309

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.060
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2359536; hg19: chr10-20899608;