14-88971072-A-G

Variant names:

• chr14-88971072-A-G
• rs12589060

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 0.559 in 152,012 control chromosomes in the GnomAD database, including 23,962 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 0.56 (23962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84927 AN: 151894 Hom.: 23934 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.559 AC: 84999 AN: 152012 Hom.: 23962 Cov.: 32 AF XY: 0.557 AC XY: 41395 AN XY: 74314

African (AFR) AF: 0.525 AC: 21768 AN: 41452

American (AMR) AF: 0.493 AC: 7531 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5170

South Asian (SAS) AF: 0.517 AC: 2487 AN: 4812

European-Finnish (FIN) AF: 0.634 AC: 6718 AN: 10594

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40306 AN: 67926

Other (OTH) AF: 0.566 AC: 1197 AN: 2114

Alfa AF: 0.568 Hom.: 11447

Bravo AF: 0.546

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.44
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs12589060; hg19: chr14-89437416;