rs2830881

Positions:

• chr21-27363488-C-T
• chr21-27363488-C-A

Variant summary

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

The XR_007067831.1(LOC124905003):​n.1045G>A 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 0.468 in 151,976 control chromosomes in the GnomAD database, including 18,561 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 0.47 (18561 hom., cov: 33)
• Consequence: LOC124905003 XR_007067831.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

ENSG00000231236 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905003	XR_007067831.1	n.1045G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231236	ENST00000420186.2	n.332-2332G>A		intron_variant		1
ENSG00000236332	ENST00000447384.1	n.391+675C>T		intron_variant		1
ENSG00000236332	ENST00000656258.1	n.434+675C>T		intron_variant
ENSG00000236332	ENST00000666822.1	n.399+675C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71058 AN: 151858 Hom.: 18542 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.468 AC: 71094 AN: 151976 Hom.: 18561 Cov.: 33 AF XY: 0.462 AC XY: 34329 AN XY: 74270

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.471

Alfa AF: 0.524 Hom.: 3677

Bravo AF: 0.448

Asia WGS AF: 0.350 AC: 1209 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2830881; hg19: chr21-28735807;