5-166530081-T-G

Variant names:

• chr5-166530081-T-G
• rs2122554

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 0.836 in 152,030 control chromosomes in the GnomAD database, including 55,565 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 0.84 (55565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127080 AN: 151912 Hom.: 55542 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.836 AC: 127149 AN: 152030 Hom.: 55565 Cov.: 32 AF XY: 0.841 AC XY: 62465 AN XY: 74316

African (AFR) AF: 0.556 AC: 23053 AN: 41464

American (AMR) AF: 0.889 AC: 13572 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3185 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4056 AN: 5158

South Asian (SAS) AF: 0.899 AC: 4336 AN: 4822

European-Finnish (FIN) AF: 0.985 AC: 10447 AN: 10608

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65608 AN: 67930

Other (OTH) AF: 0.861 AC: 1814 AN: 2108

Alfa AF: 0.939 Hom.: 122410

Bravo AF: 0.817

Asia WGS AF: 0.839 AC: 2916 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2122554; hg19: chr5-165957086;