XR_007067897.1:n.766G>C

Variant names:

• chr21-43813437-G-C
• rs2838393
• XR_007067897.1:n.766G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007067897.1(LOC124905033):​n.766G>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 0.284 in 151,814 control chromosomes in the GnomAD database, including 6,927 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 0.28 (6927 hom., cov: 32)
• Consequence: LOC124905033 XR_007067897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 7 publications found

Genes affected

LOC124905033 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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: 0.284 AC: 43029 AN: 151698 Hom.: 6908 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.284 AC: 43085 AN: 151814 Hom.: 6927 Cov.: 32 AF XY: 0.287 AC XY: 21334 AN XY: 74216

African (AFR) AF: 0.389 AC: 16057 AN: 41256

American (AMR) AF: 0.340 AC: 5195 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2410 AN: 5150

South Asian (SAS) AF: 0.305 AC: 1475 AN: 4830

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10576

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13244 AN: 67930

Other (OTH) AF: 0.278 AC: 585 AN: 2106

Alfa AF: 0.243 Hom.: 651

Bravo AF: 0.297

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.47
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2838393; hg19: chr21-45233318;