chr14-21610372-G-A

Position:

• chr14-21610372-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.880

Alfa AF: 0.876 Hom.: 73763

Bravo AF: 0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10047948; hg19: chr14-22078529;