20-12668716-G-C

Position:

• chr20-12668716-G-C

Variant summary

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

The XR_007067533.1(LOC105372532):​n.235+2271C>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 0.185 in 151,960 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3008 hom., cov: 32)
• Consequence: LOC105372532 XR_007067533.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

LOC105372532 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372532	XR_007067533.1	n.235+2271C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28085 AN: 151842 Hom.: 2994 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.185 AC: 28128 AN: 151960 Hom.: 3008 Cov.: 32 AF XY: 0.186 AC XY: 13851 AN XY: 74290

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.195

Alfa AF: 0.0659 Hom.: 64

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963431; hg19: chr20-12649363;