rs10853727

Variant names:

• chr19-39249823-T-C
• rs10853727

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0816 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

Gnomad4 AFR AF: 0.0734

Gnomad4 AMR AF: 0.0627

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.0818

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0933 Hom.: 143

Bravo AF: 0.0807

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10853727; hg19: chr19-39740463;