rs9316065

Positions:

• chr13-44052645-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 0.0743 in 152,168 control chromosomes in the GnomAD database, including 1,097 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 0.074 (1097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11272 AN: 152050 Hom.: 1095 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0578

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00604

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0743 AC: 11300 AN: 152168 Hom.: 1097 Cov.: 32 AF XY: 0.0732 AC XY: 5447 AN XY: 74396

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0481

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.0475

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00604

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0473 Hom.: 190

Bravo AF: 0.0835

Asia WGS AF: 0.0630 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9316065; hg19: chr13-44626781;