rs7268640

chr20-48533730-T-C

Variant summary

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

The XR_936817.4(LOC105372646):n.793A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,232 control chromosomes in the GnomAD database, including 6,400 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 0.17 (6400 hom., cov: 32)
• Consequence: LOC105372646 XR_936817.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

LOC105372646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372646	XR_936817.4	n.793A>G		non_coding_transcript_exon_variant	3/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26316 AN: 152114 Hom.: 6364 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.173 AC: 26408 AN: 152232 Hom.: 6400 Cov.: 32 AF XY: 0.170 AC XY: 12634 AN XY: 74454

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.0690

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.0114

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0488 Hom.: 1236

Bravo AF: 0.199

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.11
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7268640; hg19: chr20-47150268;