chr14-21610372-G-A

Variant names:

• chr14-21610372-G-A
• rs10047948

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 0.875 in 152,232 control chromosomes in the GnomAD database, including 58,507 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 0.87 (58507 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.897 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: 0.875 AC: 133095 AN: 152116 Hom.: 58463 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.875 AC: 133193 AN: 152232 Hom.: 58507 Cov.: 31 AF XY: 0.875 AC XY: 65165 AN XY: 74450

African (AFR) AF: 0.905 AC: 37576 AN: 41542

American (AMR) AF: 0.848 AC: 12962 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2974 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3238 AN: 5172

South Asian (SAS) AF: 0.907 AC: 4377 AN: 4828

European-Finnish (FIN) AF: 0.900 AC: 9534 AN: 10598

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59539 AN: 68012

Other (OTH) AF: 0.880 AC: 1858 AN: 2112

Alfa AF: 0.876 Hom.: 103499

Bravo AF: 0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs10047948; hg19: chr14-22078529;