rs1927914

Variant names:

• chr9-117702447-G-A
• rs1927914

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 0.531 in 152,050 control chromosomes in the GnomAD database, including 24,124 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 0.53 (24124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.532 AC: 80777 AN: 151932 Hom.: 24131 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.531 AC: 80786 AN: 152050 Hom.: 24124 Cov.: 32 AF XY: 0.530 AC XY: 39379 AN XY: 74326

Gnomad4 AFR AF: 0.234 AC: 0.234214 AN: 0.234214

Gnomad4 AMR AF: 0.614 AC: 0.61388 AN: 0.61388

Gnomad4 ASJ AF: 0.628 AC: 0.628028 AN: 0.628028

Gnomad4 EAS AF: 0.619 AC: 0.61914 AN: 0.61914

Gnomad4 SAS AF: 0.616 AC: 0.616231 AN: 0.616231

Gnomad4 FIN AF: 0.551 AC: 0.551374 AN: 0.551374

Gnomad4 NFE AF: 0.668 AC: 0.668325 AN: 0.668325

Gnomad4 OTH AF: 0.579 AC: 0.579147 AN: 0.579147

Alfa AF: 0.631 Hom.: 20989

Bravo AF: 0.527

Asia WGS AF: 0.594 AC: 2067 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927914; hg19: chr9-120464725;