rs2820037

Variant names:

• chr1-239273242-A-T
• rs2820037

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 0.211 in 151,968 control chromosomes in the GnomAD database, including 4,101 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 0.21 (4101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.211 AC: 32002 AN: 151850 Hom.: 4106 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.211 AC: 32021 AN: 151968 Hom.: 4101 Cov.: 32 AF XY: 0.208 AC XY: 15473 AN XY: 74272

African (AFR) AF: 0.358 AC: 14816 AN: 41422

American (AMR) AF: 0.191 AC: 2920 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.0695 AC: 358 AN: 5152

South Asian (SAS) AF: 0.148 AC: 711 AN: 4812

European-Finnish (FIN) AF: 0.129 AC: 1361 AN: 10578

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10473 AN: 67966

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.178 Hom.: 357

Bravo AF: 0.221

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2820037; hg19: chr1-239436542;