rs2836333

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr21-38352778-A-G
• chr21-38352778-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985513	XR_001755040.2	n.672A>G		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: 0.610 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 v4.3

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;