21-25864303-A-C

Position:

• chr21-25864303-A-C

Variant summary

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

The XR_007067828.1(LOC105372756):​n.657A>C 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 0.537 in 151,984 control chromosomes in the GnomAD database, including 22,163 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 0.54 (22163 hom., cov: 32)
• Consequence: LOC105372756 XR_007067828.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

LOC105372756 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372756	XR_007067828.1	n.657A>C		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81559 AN: 151866 Hom.: 22128 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.537 AC: 81652 AN: 151984 Hom.: 22163 Cov.: 32 AF XY: 0.540 AC XY: 40067 AN XY: 74258

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.509

Alfa AF: 0.505 Hom.: 8661

Bravo AF: 0.553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8126493; hg19: chr21-27236614;