10-49669219-A-G

Variant names:

• chr10-49669219-A-G
• rs867687

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 0.184 in 151,924 control chromosomes in the GnomAD database, including 3,131 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 0.18 (3131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 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: 0.184 AC: 27959 AN: 151804 Hom.: 3135 Cov.: 31

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0769

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.184 AC: 27949 AN: 151924 Hom.: 3131 Cov.: 31 AF XY: 0.188 AC XY: 13930 AN XY: 74260

African (AFR) AF: 0.0547 AC: 2269 AN: 41462

American (AMR) AF: 0.216 AC: 3292 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3470

East Asian (EAS) AF: 0.0765 AC: 394 AN: 5152

South Asian (SAS) AF: 0.199 AC: 958 AN: 4810

European-Finnish (FIN) AF: 0.279 AC: 2937 AN: 10530

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16515 AN: 67922

Other (OTH) AF: 0.218 AC: 459 AN: 2104

Alfa AF: 0.217 Hom.: 8018

Bravo AF: 0.174

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.72
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs867687; hg19: chr10-50877265;