20-47796832-G-T

Variant names:

• chr20-47796832-G-T
• rs13038095
• XR_001754648.3:n.319-1625G>T

Variant summary

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

The XR_001754648.3(LOC107985401):​n.319-1625G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,250 control chromosomes in the GnomAD database, including 1,033 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 0.11 (1033 hom., cov: 33)
• Consequence: LOC107985401 XR_001754648.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

LOC107985401 (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 = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985401	XR_001754648.3	n.319-1625G>T		intron_variant	Intron 1 of 1
LOC124904921	XR_007067619.1	n.189+112C>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16972 AN: 152132 Hom.: 1033 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.112 AC: 16985 AN: 152250 Hom.: 1033 Cov.: 33 AF XY: 0.111 AC XY: 8252 AN XY: 74446

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.0528

Gnomad4 EAS AF: 0.0204

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0922

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0867 Hom.: 724

Bravo AF: 0.112

Asia WGS AF: 0.0440 AC: 154 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	6.4
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13038095; hg19: chr20-46425576;