21-27363488-C-T

Variant names:

• chr21-27363488-C-T
• rs2830881
• ENST00000420186.2:n.332-2332G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000231236 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420186.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231236	ENST00000420186.2	TSL:1	n.332-2332G>A		intron	N/A
	ENSG00000236332	ENST00000447384.1	TSL:1	n.391+675C>T		intron	N/A
	ENSG00000236332	ENST00000656258.2		n.434+675C>T		intron	N/A

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

African (AFR) AF: 0.252 AC: 10462 AN: 41492

American (AMR) AF: 0.461 AC: 7030 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3468

East Asian (EAS) AF: 0.191 AC: 987 AN: 5166

South Asian (SAS) AF: 0.571 AC: 2753 AN: 4820

European-Finnish (FIN) AF: 0.495 AC: 5220 AN: 10546

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.608 AC: 41300 AN: 67920

Other (OTH) AF: 0.471 AC: 993 AN: 2110

Alfa AF: 0.516 Hom.: 3705

Bravo AF: 0.448

Asia WGS AF: 0.350 AC: 1209 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.4
DANN	Benign	0.49
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs2830881; hg19: chr21-28735807;