rs8001767

chr13-73242688-G-A

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 0.371 in 151,952 control chromosomes in the GnomAD database, including 11,227 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 0.37 (11227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 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: 0.371 AC: 56307 AN: 151834 Hom.: 11225 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0460

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.371 AC: 56324 AN: 151952 Hom.: 11227 Cov.: 32 AF XY: 0.364 AC XY: 27050 AN XY: 74250

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0467

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.377

Alfa AF: 0.430 Hom.: 29532

Bravo AF: 0.356

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.0
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8001767; hg19: chr13-73816825;