rs2838271

Variant names:

• chr21-43341994-G-A
• rs2838271
• ENST00000849138.1:n.309+2045C>T

Variant summary

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

The ENST00000849138.1(ENSG00000310337):​n.309+2045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,954 control chromosomes in the GnomAD database, including 3,951 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 0.23 (3951 hom., cov: 33)
• Consequence: ENSG00000310337 ENST00000849138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 1 publications found

Genes affected

ENSG00000310337 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310337	ENST00000849138.1	n.309+2045C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34183 AN: 151834 Hom.: 3947 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.225 AC: 34220 AN: 151954 Hom.: 3951 Cov.: 33 AF XY: 0.220 AC XY: 16328 AN XY: 74272

African (AFR) AF: 0.260 AC: 10769 AN: 41452

American (AMR) AF: 0.188 AC: 2876 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3466

East Asian (EAS) AF: 0.162 AC: 836 AN: 5162

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1650 AN: 10590

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15216 AN: 67862

Other (OTH) AF: 0.222 AC: 469 AN: 2112

Alfa AF: 0.228 Hom.: 6900

Bravo AF: 0.227

Asia WGS AF: 0.183 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs2838271; hg19: chr21-44761874;