rs12970791

chr18-65498567-G-T

Variant summary

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

The XR_935583.2(LOC105372169):n.211C>A 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 0.394 in 151,318 control chromosomes in the GnomAD database, including 12,223 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 0.39 (12223 hom., cov: 31)
• Consequence: LOC105372169 XR_935583.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

LOC105372169 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372169	XR_935583.2	n.211C>A		non_coding_transcript_exon_variant	2/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59578 AN: 151200 Hom.: 12219 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.394 AC: 59591 AN: 151318 Hom.: 12223 Cov.: 31 AF XY: 0.394 AC XY: 29103 AN XY: 73878

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.403

Alfa AF: 0.399 Hom.: 2053

Bravo AF: 0.392

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.6
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12970791; hg19: chr18-63165803;