rs2838705

Variant names:

• chr21-44849199-C-G
• rs2838705

Your query was ambiguous. Multiple possible variants found:

• chr21-44849199-C-G
• chr21-44849199-C-T

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 0.152 in 152,160 control chromosomes in the GnomAD database, including 2,428 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 0.15 (2428 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.152 AC: 23091 AN: 152042 Hom.: 2426 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.152 AC: 23118 AN: 152160 Hom.: 2428 Cov.: 33 AF XY: 0.156 AC XY: 11617 AN XY: 74398

African (AFR) AF: 0.241 AC: 9984 AN: 41482

American (AMR) AF: 0.203 AC: 3104 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2232 AN: 5170

South Asian (SAS) AF: 0.0772 AC: 373 AN: 4832

European-Finnish (FIN) AF: 0.173 AC: 1833 AN: 10594

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0744 AC: 5056 AN: 68000

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.112 Hom.: 163

Bravo AF: 0.166

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2838705; hg19: chr21-46269114; COSMIC: COSV58366901;