14-90410483-A-T

Variant names:

• chr14-90410483-A-T
• rs6575134

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 0.913 in 152,244 control chromosomes in the GnomAD database, including 63,735 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 0.91 (63735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 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: 0.913 AC: 138887 AN: 152126 Hom.: 63703 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.913 AC: 138973 AN: 152244 Hom.: 63735 Cov.: 32 AF XY: 0.914 AC XY: 68012 AN XY: 74438

African (AFR) AF: 0.814 AC: 33809 AN: 41514

American (AMR) AF: 0.942 AC: 14406 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3233 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4684 AN: 5178

South Asian (SAS) AF: 0.923 AC: 4462 AN: 4832

European-Finnish (FIN) AF: 0.958 AC: 10159 AN: 10600

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65124 AN: 68036

Other (OTH) AF: 0.911 AC: 1926 AN: 2114

Alfa AF: 0.936 Hom.: 8319

Bravo AF: 0.907

Asia WGS AF: 0.898 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs6575134; hg19: chr14-90876827;