rs2838751

Variant names:

• chr21-44988875-G-A
• rs2838751

Variant summary

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

The variant allele was found at a frequency of 0.118 in 152,138 control chromosomes in the GnomAD database, including 1,130 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 0.12 (1130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17963 AN: 152020 Hom.: 1132 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.118 AC: 17965 AN: 152138 Hom.: 1130 Cov.: 32 AF XY: 0.120 AC XY: 8902 AN XY: 74378

African (AFR) AF: 0.108 AC: 4463 AN: 41516

American (AMR) AF: 0.172 AC: 2630 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3470

East Asian (EAS) AF: 0.108 AC: 560 AN: 5170

South Asian (SAS) AF: 0.0388 AC: 187 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1414 AN: 10586

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7847 AN: 67978

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.117 Hom.: 2182

Bravo AF: 0.122

Asia WGS AF: 0.0850 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.5
DANN	Benign	0.52
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs2838751; hg19: chr21-46408790;