rs1564525

Positions:

• chr14-84670992-T-C
• chr14-84670992-T-G

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 0.132 in 152,150 control chromosomes in the GnomAD database, including 1,611 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 0.13 (1611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20004 AN: 152032 Hom.: 1606 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.132 AC: 20021 AN: 152150 Hom.: 1611 Cov.: 32 AF XY: 0.134 AC XY: 9987 AN XY: 74358

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0661

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.131

Alfa AF: 0.103 Hom.: 458

Bravo AF: 0.144

Asia WGS AF: 0.212 AC: 736 AN: 3478

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	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564525; hg19: chr14-85137336;