rs1417594

Variant names:

• chr14-94892441-A-G
• rs1417594

Your query was ambiguous. Multiple possible variants found:

• chr14-94892441-A-G
• chr14-94892441-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 0.229 in 152,090 control chromosomes in the GnomAD database, including 5,383 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 0.23 (5383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 1 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 = 0.437 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: 0.229 AC: 34822 AN: 151972 Hom.: 5372 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.229 AC: 34885 AN: 152090 Hom.: 5383 Cov.: 32 AF XY: 0.229 AC XY: 17019 AN XY: 74354

African (AFR) AF: 0.442 AC: 18318 AN: 41448

American (AMR) AF: 0.172 AC: 2629 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.130 AC: 669 AN: 5164

South Asian (SAS) AF: 0.241 AC: 1163 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1692 AN: 10598

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9570 AN: 67986

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.222 Hom.: 710

Bravo AF: 0.238

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.021
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1417594; hg19: chr14-95358778;