rs10853727

Variant names:

• chr19-39249823-T-C
• rs10853727

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 0.0816 in 152,234 control chromosomes in the GnomAD database, including 543 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 0.082 (543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0923 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12410 AN: 152116 Hom.: 543 Cov.: 32

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0629

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0501

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0816 AC: 12420 AN: 152234 Hom.: 543 Cov.: 32 AF XY: 0.0802 AC XY: 5973 AN XY: 74432

African (AFR) AF: 0.0734 AC: 3048 AN: 41548

American (AMR) AF: 0.0627 AC: 959 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5178

South Asian (SAS) AF: 0.0506 AC: 244 AN: 4824

European-Finnish (FIN) AF: 0.0818 AC: 867 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6408 AN: 68012

Other (OTH) AF: 0.0822 AC: 174 AN: 2116

Alfa AF: 0.0940 Hom.: 245

Bravo AF: 0.0807

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.39
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10853727; hg19: chr19-39740463;