rs2029167

Variant names:

• chr12-54196349-G-A
• rs2029167
• XR_944983.1:n.367-4111G>A

Variant summary

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

The XR_944983.1(LOC105369777):​n.367-4111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,854 control chromosomes in the GnomAD database, including 20,610 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 0.52 (20610 hom., cov: 31)
• Consequence: LOC105369777 XR_944983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 6 publications found

Genes affected

LOC105369777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369777	XR_944983.1	n.367-4111G>A		intron_variant	Intron 3 of 3
LOC105369777	XR_944984.2	n.194-4111G>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78735 AN: 151736 Hom.: 20600 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.519 AC: 78778 AN: 151854 Hom.: 20610 Cov.: 31 AF XY: 0.524 AC XY: 38903 AN XY: 74180

African (AFR) AF: 0.488 AC: 20192 AN: 41384

American (AMR) AF: 0.488 AC: 7441 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2581 AN: 5128

South Asian (SAS) AF: 0.622 AC: 2999 AN: 4818

European-Finnish (FIN) AF: 0.615 AC: 6473 AN: 10528

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35647 AN: 67954

Other (OTH) AF: 0.501 AC: 1058 AN: 2110

Alfa AF: 0.517 Hom.: 2549

Bravo AF: 0.505

Asia WGS AF: 0.521 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.5
DANN	Benign	0.72
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2029167; hg19: chr12-54590133;