rs2949535

Variant names:

• chr18-30277820-A-G
• rs2949535

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 0.234 in 150,444 control chromosomes in the GnomAD database, including 4,692 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 (4692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35167 AN: 150326 Hom.: 4685 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.234 AC: 35176 AN: 150444 Hom.: 4692 Cov.: 31 AF XY: 0.228 AC XY: 16775 AN XY: 73486

African (AFR) AF: 0.116 AC: 4803 AN: 41306

American (AMR) AF: 0.232 AC: 3473 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1290 AN: 3436

East Asian (EAS) AF: 0.207 AC: 1055 AN: 5094

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4810

European-Finnish (FIN) AF: 0.215 AC: 2263 AN: 10544

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20252 AN: 66978

Other (OTH) AF: 0.246 AC: 512 AN: 2078

Alfa AF: 0.282 Hom.: 3352

Bravo AF: 0.233

Asia WGS AF: 0.245 AC: 852 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.74
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2949535; hg19: chr18-27857785;