chr6-13562045-G-T

Variant names:

• chr6-13562045-G-T
• rs16874223

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 0.0726 in 152,082 control chromosomes in the GnomAD database, including 514 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 0.073 (514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.127 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: 0.0724 AC: 10995 AN: 151966 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0726 AC: 11043 AN: 152082 Hom.: 514 Cov.: 32 AF XY: 0.0730 AC XY: 5429 AN XY: 74334

African (AFR) AF: 0.106 AC: 4409 AN: 41434

American (AMR) AF: 0.132 AC: 2017 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3468

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5186

South Asian (SAS) AF: 0.0537 AC: 259 AN: 4826

European-Finnish (FIN) AF: 0.0419 AC: 443 AN: 10578

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0496 AC: 3374 AN: 67992

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0606 Hom.: 1075

Bravo AF: 0.0825

Asia WGS AF: 0.0490 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.61
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs16874223; hg19: chr6-13562277;