chr19-10381501-A-C

Variant names:

• chr19-10381501-A-C
• rs891696485

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.00085 (0 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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: 0.000848 AC: 92 AN: 108512 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000787

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000716

Gnomad ASJ AF: 0.00223

Gnomad EAS AF: 0.000532

Gnomad SAS AF: 0.00117

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000651

Gnomad OTH AF: 0.000651

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000848 AC: 92 AN: 108502 Hom.: 0 Cov.: 29 AF XY: 0.000912 AC XY: 47 AN XY: 51558

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000786 AC: 23 AN: 29252

American (AMR) AF: 0.000715 AC: 8 AN: 11186

Ashkenazi Jewish (ASJ) AF: 0.00223 AC: 6 AN: 2692

East Asian (EAS) AF: 0.000533 AC: 2 AN: 3750

South Asian (SAS) AF: 0.00118 AC: 4 AN: 3400

European-Finnish (FIN) AF: 0.00292 AC: 15 AN: 5144

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 174

European-Non Finnish (NFE) AF: 0.000652 AC: 33 AN: 50648

Other (OTH) AF: 0.000648 AC: 1 AN: 1544

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs891696485; hg19: chr19-10492177;