rs1243519

Variant names:

• chr14-94834020-A-G
• rs1243519

Your query was ambiguous. Multiple possible variants found:

• chr14-94834020-A-G
• chr14-94834020-A-T

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 0.155 in 150,966 control chromosomes in the GnomAD database, including 1,905 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 0.15 (1905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.155 AC: 23334 AN: 150850 Hom.: 1907 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0989

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.155 AC: 23340 AN: 150966 Hom.: 1905 Cov.: 31 AF XY: 0.159 AC XY: 11680 AN XY: 73650

African (AFR) AF: 0.137 AC: 5619 AN: 40990

American (AMR) AF: 0.135 AC: 2042 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3464

East Asian (EAS) AF: 0.0992 AC: 504 AN: 5082

South Asian (SAS) AF: 0.331 AC: 1572 AN: 4748

European-Finnish (FIN) AF: 0.172 AC: 1797 AN: 10432

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10557 AN: 67852

Other (OTH) AF: 0.165 AC: 344 AN: 2088

Alfa AF: 0.154 Hom.: 3165

Bravo AF: 0.146

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1243519; hg19: chr14-95300357;