rs9571178

chr13-64362111-G-Achr13-64362111-G-T

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 0.429 in 151,612 control chromosomes in the GnomAD database, including 14,399 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 0.43 (14399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 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: 0.429 AC: 65011 AN: 151494 Hom.: 14376 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.429 AC: 65088 AN: 151612 Hom.: 14399 Cov.: 31 AF XY: 0.425 AC XY: 31441 AN XY: 74062

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.435

Alfa AF: 0.449 Hom.: 31071

Bravo AF: 0.445

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	2.1
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9571178; hg19: chr13-64936243;