14-60572758-A-G

Variant names:

• chr14-60572758-A-G
• rs10483726

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 0.834 in 152,194 control chromosomes in the GnomAD database, including 54,282 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 0.83 (54282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126832 AN: 152076 Hom.: 54252 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.834 AC: 126916 AN: 152194 Hom.: 54282 Cov.: 32 AF XY: 0.836 AC XY: 62242 AN XY: 74414

African (AFR) AF: 0.633 AC: 26216 AN: 41444

American (AMR) AF: 0.893 AC: 13662 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3123 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4426 AN: 5184

South Asian (SAS) AF: 0.756 AC: 3645 AN: 4820

European-Finnish (FIN) AF: 0.974 AC: 10350 AN: 10622

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62599 AN: 68030

Other (OTH) AF: 0.847 AC: 1790 AN: 2114

Alfa AF: 0.891 Hom.: 15095

Bravo AF: 0.821

Asia WGS AF: 0.808 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.76
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10483726; hg19: chr14-61039476;