chr20-11324543-T-C

Position:

• chr20-11324543-T-C

Variant summary

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

The XR_937261.2(LOC105372529):​n.552-11383A>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 0.217 in 152,158 control chromosomes in the GnomAD database, including 4,121 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 0.22 (4121 hom., cov: 33)
• Consequence: LOC105372529 XR_937261.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753

Genes affected

LOC105372529 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372529	XR_937261.2	n.552-11383A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32961 AN: 152040 Hom.: 4118 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.217 AC: 32979 AN: 152158 Hom.: 4121 Cov.: 33 AF XY: 0.215 AC XY: 16023 AN XY: 74380

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.229

Alfa AF: 0.258 Hom.: 7315

Bravo AF: 0.220

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485747; hg19: chr20-11305191;