rs8001767

Variant names:

• chr13-73242688-G-A
• rs8001767

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;