rs891696485

Variant names:

• chr19-10381501-A-C
• rs891696485

Your query was ambiguous. Multiple possible variants found:

• chr19-10381501-A-C
• chr19-10381501-A-T

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).

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: 0.000848 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 v4.3

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;