rs2827837

Variant names:

• chr21-23086603-T-C
• rs2827837
• ENST00000421604.1:n.297+18567T>C

Variant summary

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

The ENST00000421604.1(ENSG00000230972):​n.297+18567T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,292 control chromosomes in the GnomAD database, including 666 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 0.077 (666 hom., cov: 32)
• Consequence: ENSG00000230972 ENST00000421604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 2 publications found

Genes affected

ENSG00000230972 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421604.1. 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
	ENSG00000230972	ENST00000421604.1	TSL:3	n.297+18567T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0774 AC: 11786 AN: 152178 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0335

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0774 AC: 11792 AN: 152292 Hom.: 666 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74458

African (AFR) AF: 0.156 AC: 6474 AN: 41556

American (AMR) AF: 0.0526 AC: 805 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0358 AC: 124 AN: 3468

East Asian (EAS) AF: 0.151 AC: 784 AN: 5182

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4828

European-Finnish (FIN) AF: 0.0183 AC: 195 AN: 10628

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0448 AC: 3046 AN: 68014

Other (OTH) AF: 0.0830 AC: 175 AN: 2108

Alfa AF: 0.0662 Hom.: 77

Bravo AF: 0.0856

Asia WGS AF: 0.0730 AC: 256 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.79
DANN	Benign	0.90
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2827837; hg19: chr21-24458925;