21-43813437-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905033	XR_007067897.1	n.766G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;