chr12-29993079-C-T

Variant names:

• chr12-29993079-C-T
• rs1909160
• XR_001749060.1:n.313+20673G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749060.1(LOC105369715):​n.313+20673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,982 control chromosomes in the GnomAD database, including 13,728 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 0.41 (13728 hom., cov: 32)
• Consequence: LOC105369715 XR_001749060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 6 publications found

Genes affected

LOC105369715 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369715	XR_001749060.1	n.313+20673G>A		intron_variant	Intron 3 of 5
LOC105369715	XR_001749061.1	n.313+20673G>A		intron_variant	Intron 3 of 4
LOC105369715	XR_931474.1	n.313+20673G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62439 AN: 151864 Hom.: 13720 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.411 AC: 62459 AN: 151982 Hom.: 13728 Cov.: 32 AF XY: 0.409 AC XY: 30370 AN XY: 74270

African (AFR) AF: 0.278 AC: 11543 AN: 41450

American (AMR) AF: 0.546 AC: 8339 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1217 AN: 5158

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4820

European-Finnish (FIN) AF: 0.397 AC: 4189 AN: 10554

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32675 AN: 67948

Other (OTH) AF: 0.447 AC: 944 AN: 2110

Alfa AF: 0.438 Hom.: 5380

Bravo AF: 0.420

Asia WGS AF: 0.294 AC: 1025 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs1909160; hg19: chr12-30146012;