14-85276277-G-T

Variant names:

• chr14-85276277-G-T
• rs10498582

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 0.57 in 151,586 control chromosomes in the GnomAD database, including 25,689 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 0.57 (25689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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: 0.570 AC: 86274 AN: 151468 Hom.: 25664 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.0926

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.570 AC: 86347 AN: 151586 Hom.: 25689 Cov.: 32 AF XY: 0.563 AC XY: 41708 AN XY: 74066

African (AFR) AF: 0.697 AC: 28851 AN: 41396

American (AMR) AF: 0.494 AC: 7503 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1918 AN: 3460

East Asian (EAS) AF: 0.0928 AC: 476 AN: 5130

South Asian (SAS) AF: 0.362 AC: 1740 AN: 4808

European-Finnish (FIN) AF: 0.584 AC: 6161 AN: 10542

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 37959 AN: 67750

Other (OTH) AF: 0.535 AC: 1124 AN: 2100

Alfa AF: 0.503 Hom.: 1676

Bravo AF: 0.568

Asia WGS AF: 0.255 AC: 889 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.59
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10498582; hg19: chr14-85742621;