rs2838891

Positions:

• chr21-45351569-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000689879.2(ENSG00000289448):​n.143-1796G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,188 control chromosomes in the GnomAD database, including 11,567 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 0.38 (11567 hom., cov: 35)
• Consequence: ENST00000689879.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372839	XR_937800.3	n.122-1796G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689879.2	n.143-1796G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57060 AN: 152070 Hom.: 11566 Cov.: 35

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.375 AC: 57078 AN: 152188 Hom.: 11567 Cov.: 35 AF XY: 0.373 AC XY: 27720 AN XY: 74404

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.393

Alfa AF: 0.445 Hom.: 9588

Bravo AF: 0.368

Asia WGS AF: 0.343 AC: 1190 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	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838891; hg19: chr21-46771484;