19-2714172-T-C

Variant names:

• chr19-2714172-T-C
• rs185543003

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.014 (76 hom., cov: 9)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0143 AC: 880 AN: 61602 Hom.: 76 Cov.: 9

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00972

Gnomad ASJ AF: 0.000480

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000716

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00833

Gnomad NFE AF: 0.000635

Gnomad OTH AF: 0.0113

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

GnomAD4 genome AF: 0.0143 AC: 883 AN: 61626 Hom.: 76 Cov.: 9 AF XY: 0.0146 AC XY: 424 AN XY: 28952

African (AFR) AF: 0.124 AC: 787 AN: 6370

American (AMR) AF: 0.00970 AC: 58 AN: 5978

Ashkenazi Jewish (ASJ) AF: 0.000480 AC: 1 AN: 2084

East Asian (EAS) AF: 0.00 AC: 0 AN: 1056

South Asian (SAS) AF: 0.000717 AC: 1 AN: 1394

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3910

Middle Eastern (MID) AF: 0.00893 AC: 1 AN: 112

European-Non Finnish (NFE) AF: 0.000635 AC: 25 AN: 39398

Other (OTH) AF: 0.0112 AC: 10 AN: 896

Alfa AF: 0.0232 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs185543003; hg19: chr19-2714170;