19-10509950-G-C

Variant names:

• chr19-10509950-G-C
• rs2007529

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 0.199 in 151,034 control chromosomes in the GnomAD database, including 3,407 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 0.20 (3407 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 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: 0.198 AC: 29946 AN: 150922 Hom.: 3399 Cov.: 30

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.199 AC: 29981 AN: 151034 Hom.: 3407 Cov.: 30 AF XY: 0.200 AC XY: 14770 AN XY: 73722

African (AFR) AF: 0.306 AC: 12600 AN: 41166

American (AMR) AF: 0.132 AC: 1993 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3462

East Asian (EAS) AF: 0.0464 AC: 236 AN: 5088

South Asian (SAS) AF: 0.218 AC: 1041 AN: 4766

European-Finnish (FIN) AF: 0.239 AC: 2476 AN: 10368

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10370 AN: 67748

Other (OTH) AF: 0.197 AC: 413 AN: 2094

Alfa AF: 0.0743 Hom.: 104

Bravo AF: 0.194

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.56
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2007529; hg19: chr19-10620626;