chr16-55205130-T-G

Variant names:

• chr16-55205130-T-G
• rs2631530

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 0.913 in 152,264 control chromosomes in the GnomAD database, including 63,578 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 0.91 (63578 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 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: 0.913 AC: 138872 AN: 152144 Hom.: 63540 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.913 AC: 138966 AN: 152264 Hom.: 63578 Cov.: 33 AF XY: 0.910 AC XY: 67744 AN XY: 74444

African (AFR) AF: 0.847 AC: 35180 AN: 41524

American (AMR) AF: 0.879 AC: 13457 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3361 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4483 AN: 5168

South Asian (SAS) AF: 0.871 AC: 4206 AN: 4828

European-Finnish (FIN) AF: 0.933 AC: 9910 AN: 10616

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65261 AN: 68038

Other (OTH) AF: 0.922 AC: 1950 AN: 2114

Alfa AF: 0.928 Hom.: 11420

Bravo AF: 0.909

Asia WGS AF: 0.865 AC: 3006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.98
DANN	Benign	0.52
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2631530; hg19: chr16-55239042;