rs12143943

Positions:

• chr1-204602943-G-A

Variant summary

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

The XR_007066814.1(LOC105371692):​n.16571G>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 0.399 in 151,966 control chromosomes in the GnomAD database, including 13,292 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 0.40 (13286 hom., cov: 31)
  • Exomes 𝑓: 0.50 (6 hom.)
• Consequence: LOC105371692 XR_007066814.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

Genes affected

LOC105371692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371692	XR_007066814.1	n.16571G>A		non_coding_transcript_exon_variant	7/13

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60512 AN: 151802 Hom.: 13278 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.500 AC: 23 AN: 46 Hom.: 6 AF XY: 0.500 AC XY: 19 AN XY: 38

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.526

GnomAD4 genome AF: 0.399 AC: 60551 AN: 151920 Hom.: 13286 Cov.: 31 AF XY: 0.402 AC XY: 29851 AN XY: 74246

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.400

Alfa AF: 0.449 Hom.: 33571

Bravo AF: 0.388

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.062
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12143943; hg19: chr1-204572071;