XR_007067828.1:n.657A>C

Variant names:

• chr21-25864303-A-C
• rs8126493
• XR_007067828.1:n.657A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC105372756 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.584 AC: 24212 AN: 41440

American (AMR) AF: 0.504 AC: 7694 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1637 AN: 3472

East Asian (EAS) AF: 0.446 AC: 2300 AN: 5162

South Asian (SAS) AF: 0.586 AC: 2817 AN: 4810

European-Finnish (FIN) AF: 0.553 AC: 5829 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35385 AN: 67956

Other (OTH) AF: 0.509 AC: 1076 AN: 2114

Alfa AF: 0.508 Hom.: 9834

Bravo AF: 0.553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.38
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs8126493; hg19: chr21-27236614;