rs767210

Positions:

• chr13-110817691-G-A
• chr13-110817691-G-C

Variant summary

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

The NR_158538.1(LOC105370362):​n.70-1099G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,224 control chromosomes in the GnomAD database, including 1,025 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 0.10 (1025 hom., cov: 33)
• Consequence: LOC105370362 NR_158538.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

Genes affected

LOC105370362 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370362	NR_158538.1	n.70-1099G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15285 AN: 152106 Hom.: 1030 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.100 AC: 15275 AN: 152224 Hom.: 1025 Cov.: 33 AF XY: 0.102 AC XY: 7592 AN XY: 74432

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.123 Hom.: 2000

Bravo AF: 0.0859

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs767210; hg19: chr13-111470038;