rs2837066

Variant names:

• chr21-39522634-C-T
• rs2837066

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 0.145 in 152,068 control chromosomes in the GnomAD database, including 3,238 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 (3238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.145 AC: 22019 AN: 151948 Hom.: 3221 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.145 AC: 22072 AN: 152068 Hom.: 3238 Cov.: 32 AF XY: 0.141 AC XY: 10505 AN XY: 74360

African (AFR) AF: 0.378 AC: 15643 AN: 41428

American (AMR) AF: 0.0868 AC: 1327 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5172

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4820

European-Finnish (FIN) AF: 0.0341 AC: 361 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0547 AC: 3718 AN: 67992

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.0807 Hom.: 473

Bravo AF: 0.159

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2837066; hg19: chr21-40894561;