rs9317414

chr13-64325507-T-C

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 0.332 in 151,530 control chromosomes in the GnomAD database, including 9,050 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 0.33 (9050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 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: 0.332 AC: 50323 AN: 151410 Hom.: 9034 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.332 AC: 50377 AN: 151530 Hom.: 9050 Cov.: 32 AF XY: 0.329 AC XY: 24337 AN XY: 74046

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.354

Alfa AF: 0.381 Hom.: 1960

Bravo AF: 0.342

Asia WGS AF: 0.316 AC: 1090 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317414; hg19: chr13-64899639;