rs1837842

Variant names:

• chr8-20010779-T-C
• rs1837842

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 0.227 in 152,134 control chromosomes in the GnomAD database, including 4,133 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 (4133 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 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: 0.228 AC: 34614 AN: 152016 Hom.: 4135 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.227 AC: 34608 AN: 152134 Hom.: 4133 Cov.: 33 AF XY: 0.227 AC XY: 16872 AN XY: 74384

African (AFR) AF: 0.146 AC: 6077 AN: 41508

American (AMR) AF: 0.232 AC: 3547 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1071 AN: 5178

South Asian (SAS) AF: 0.213 AC: 1027 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2630 AN: 10566

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18284 AN: 67990

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.209 Hom.: 1016

Bravo AF: 0.222

Asia WGS AF: 0.224 AC: 778 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.88
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1837842; hg19: chr8-19868290;