rs17737309

chr14-84892892-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0705 in 152,252 control chromosomes in the GnomAD database, including 490 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 0.071 (490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10744 AN: 152134 Hom.: 491 Cov.: 32

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0705 AC: 10741 AN: 152252 Hom.: 490 Cov.: 32 AF XY: 0.0684 AC XY: 5094 AN XY: 74462

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0413

Gnomad4 SAS AF: 0.0694

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0805 Hom.: 112

Bravo AF: 0.0688

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17737309; hg19: chr14-85359236;