rs11063543

chr12-5162958-A-Cchr12-5162958-A-G

Variant summary

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

The XR_931577.2(LOC105369617):n.614+2573A>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 0.161 in 152,260 control chromosomes in the GnomAD database, including 2,062 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 0.16 (2062 hom., cov: 32)
• Consequence: LOC105369617 XR_931577.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

Genes affected

LOC105369617 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369617	XR_931577.2	n.614+2573A>C		intron_variant, non_coding_transcript_variant
LOC105369617	XR_001748970.2	n.587+2573A>C		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063177.1	n.561+2573A>C		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063178.1	n.570+2573A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24429 AN: 152142 Hom.: 2056 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.161 AC: 24458 AN: 152260 Hom.: 2062 Cov.: 32 AF XY: 0.159 AC XY: 11866 AN XY: 74456

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.150

Alfa AF: 0.153 Hom.: 1691

Bravo AF: 0.158

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11063543; hg19: chr12-5272124;