4-68672015-T-G

Variant names:

• chr4-68672015-T-G
• rs13112099

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 0.531 in 151,982 control chromosomes in the GnomAD database, including 21,841 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 0.53 (21841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.531 AC: 80587 AN: 151864 Hom.: 21798 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.531 AC: 80687 AN: 151982 Hom.: 21841 Cov.: 31 AF XY: 0.534 AC XY: 39658 AN XY: 74272

African (AFR) AF: 0.608 AC: 25205 AN: 41446

American (AMR) AF: 0.583 AC: 8905 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2884 AN: 5128

South Asian (SAS) AF: 0.450 AC: 2166 AN: 4818

European-Finnish (FIN) AF: 0.554 AC: 5852 AN: 10568

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32397 AN: 67964

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.514 Hom.: 2544

Bravo AF: 0.537

Asia WGS AF: 0.482 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.58
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs13112099; hg19: chr4-69537733;