21-38352778-A-G

Variant names:

• chr21-38352778-A-G
• rs2836333
• XR_001755040.2:n.672A>G

Variant summary

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

The XR_001755040.2(LOC107985513):​n.672A>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 0.611 in 151,974 control chromosomes in the GnomAD database, including 29,650 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 0.61 (29650 hom., cov: 32)
• Consequence: LOC107985513 XR_001755040.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 4 publications found

Genes affected

LOC107985513 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92679 AN: 151858 Hom.: 29595 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.611 AC: 92786 AN: 151974 Hom.: 29650 Cov.: 32 AF XY: 0.608 AC XY: 45185 AN XY: 74264

African (AFR) AF: 0.793 AC: 32870 AN: 41452

American (AMR) AF: 0.503 AC: 7684 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2439 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3883 AN: 5142

South Asian (SAS) AF: 0.690 AC: 3327 AN: 4820

European-Finnish (FIN) AF: 0.489 AC: 5156 AN: 10538

Middle Eastern (MID) AF: 0.690 AC: 200 AN: 290

European-Non Finnish (NFE) AF: 0.519 AC: 35297 AN: 67960

Other (OTH) AF: 0.615 AC: 1298 AN: 2110

Alfa AF: 0.550 Hom.: 39413

Bravo AF: 0.616

Asia WGS AF: 0.755 AC: 2627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.37
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2836333; hg19: chr21-39724700;