rs8001767

Variant names:

• chr13-73242688-G-A
• rs8001767

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.284 AC: 11775 AN: 41420

American (AMR) AF: 0.305 AC: 4657 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3472

East Asian (EAS) AF: 0.0467 AC: 241 AN: 5158

South Asian (SAS) AF: 0.231 AC: 1114 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4660 AN: 10552

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31034 AN: 67952

Other (OTH) AF: 0.377 AC: 795 AN: 2106

Alfa AF: 0.423 Hom.: 59011

Bravo AF: 0.356

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs8001767; hg19: chr13-73816825;