rs12428128

Positions:

• chr13-59497221-T-G

Variant summary

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

The XR_001749886.2(LOC107984625):​n.481-6994A>C 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 0.106 in 152,260 control chromosomes in the GnomAD database, including 929 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 0.11 (929 hom., cov: 32)
• Consequence: LOC107984625 XR_001749886.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

Genes affected

LOC107984625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984625	XR_001749886.2	n.481-6994A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16074 AN: 152142 Hom.: 931 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.106 AC: 16083 AN: 152260 Hom.: 929 Cov.: 32 AF XY: 0.102 AC XY: 7626 AN XY: 74464

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0210

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.116

Alfa AF: 0.111 Hom.: 230

Bravo AF: 0.114

Asia WGS AF: 0.0730 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12428128; hg19: chr13-60071355;