13-68558539-A-T

Variant names:

• chr13-68558539-A-T
• rs685670

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 0.0578 in 152,136 control chromosomes in the GnomAD database, including 307 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 0.058 (307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.069 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: 0.0578 AC: 8782 AN: 152018 Hom.: 305 Cov.: 31

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0212

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0578 AC: 8786 AN: 152136 Hom.: 307 Cov.: 31 AF XY: 0.0573 AC XY: 4265 AN XY: 74382

African (AFR) AF: 0.0473 AC: 1962 AN: 41504

American (AMR) AF: 0.0306 AC: 468 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3468

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5154

South Asian (SAS) AF: 0.0210 AC: 101 AN: 4808

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4807 AN: 68004

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0616 Hom.: 48

Bravo AF: 0.0513

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.57
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs685670; hg19: chr13-69132671;