14-88971072-A-G

Variant names:

• chr14-88971072-A-G
• rs12589060

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 0.559 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.559 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

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.566

Alfa AF: 0.570 Hom.: 9630

Bravo AF: 0.546

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12589060; hg19: chr14-89437416;