chr20-56151513-G-A

Position:

• chr20-56151513-G-A

Variant summary

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

The XR_936893.3(LOC105372680):​n.983-8927C>T 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 0.299 in 152,086 control chromosomes in the GnomAD database, including 7,928 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 0.30 (7928 hom., cov: 32)
• Consequence: LOC105372680 XR_936893.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

Genes affected

LOC105372680 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372680	XR_936893.3	n.983-8927C>T		intron_variant, non_coding_transcript_variant
LOC105372680	XR_001754685.2	n.1074-8927C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45427 AN: 151968 Hom.: 7902 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.299 AC: 45502 AN: 152086 Hom.: 7928 Cov.: 32 AF XY: 0.296 AC XY: 22015 AN XY: 74344

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.256

Alfa AF: 0.237 Hom.: 2434

Bravo AF: 0.303

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6513195; hg19: chr20-54726569;