13-73240754-G-T

Variant names:

• chr13-73240754-G-T
• rs11841589

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 0.306 in 152,054 control chromosomes in the GnomAD database, including 7,880 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 0.31 (7880 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46439 AN: 151938 Hom.: 7875 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.306 AC: 46475 AN: 152054 Hom.: 7880 Cov.: 33 AF XY: 0.299 AC XY: 22212 AN XY: 74348

African (AFR) AF: 0.431 AC: 17849 AN: 41430

American (AMR) AF: 0.254 AC: 3883 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1136 AN: 3470

East Asian (EAS) AF: 0.0490 AC: 254 AN: 5184

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1907 AN: 10572

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.277 AC: 18819 AN: 67980

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.276 Hom.: 3412

Bravo AF: 0.318

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.6
DANN	Benign	0.77
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs11841589; hg19: chr13-73814891;