21-42352323-A-G

Variant summary

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

The XR_937755.3(LOC105372815):n.31A>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 0.896 in 146,378 control chromosomes in the GnomAD database, including 58,751 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 0.90 (58751 hom., cov: 21)
• Consequence: LOC105372815 XR_937755.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

LOC105372815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372815	XR_937755.3	n.31A>G		non_coding_transcript_exon_variant	1/3
LOC105372815	XR_007067875.1	n.31A>G		non_coding_transcript_exon_variant	1/4
LOC105372815	XR_007067876.1	n.31A>G		non_coding_transcript_exon_variant	1/4
LOC105372815	XR_007067877.1	n.31A>G		non_coding_transcript_exon_variant	1/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.896 AC: 131029 AN: 146264 Hom.: 58702 Cov.: 21

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.896 AC: 131136 AN: 146378 Hom.: 58751 Cov.: 21 AF XY: 0.891 AC XY: 63524 AN XY: 71270

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.911

Alfa AF: 0.907 Hom.: 7298

Bravo AF: 0.897

Asia WGS AF: 0.742 AC: 2568 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225338; hg19: chr21-43772432;