rs1564525

Variant names:

• chr14-84670992-T-C
• rs1564525

Your query was ambiguous. Multiple possible variants found:

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

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 0.132 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.164 AC: 6826 AN: 41512

American (AMR) AF: 0.218 AC: 3323 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1553 AN: 5162

South Asian (SAS) AF: 0.168 AC: 811 AN: 4824

European-Finnish (FIN) AF: 0.0661 AC: 701 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0901 AC: 6128 AN: 67994

Other (OTH) AF: 0.131 AC: 277 AN: 2112

Alfa AF: 0.103 Hom.: 496

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
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs1564525; hg19: chr14-85137336;