rs10879537

Positions:

• chr12-73030218-A-G
• chr12-73030218-A-T

Variant summary

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

The XR_945088.2(LOC105369838):​n.578-12364A>G 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 0.717 in 151,844 control chromosomes in the GnomAD database, including 39,293 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 0.72 (39293 hom., cov: 31)
• Consequence: LOC105369838 XR_945088.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

LOC105369838 (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 (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369838	XR_945088.2	n.578-12364A>G		intron_variant, non_coding_transcript_variant
LOC105369838	XR_945089.2	n.527-12364A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108720 AN: 151728 Hom.: 39243 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.717 AC: 108822 AN: 151844 Hom.: 39293 Cov.: 31 AF XY: 0.715 AC XY: 53071 AN XY: 74204

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.701

Alfa AF: 0.717 Hom.: 46358

Bravo AF: 0.708

Asia WGS AF: 0.630 AC: 2193 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	0.056
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10879537; hg19: chr12-73423998;