chr5-166952767-C-T

Variant names:

• chr5-166952767-C-T
• rs3853241

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 0.0917 in 152,204 control chromosomes in the GnomAD database, including 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 0.092 (841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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: 0.0917 AC: 13950 AN: 152086 Hom.: 838 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0763

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.0917 AC: 13956 AN: 152204 Hom.: 841 Cov.: 32 AF XY: 0.0888 AC XY: 6608 AN XY: 74420

African (AFR) AF: 0.0234 AC: 974 AN: 41544

American (AMR) AF: 0.0790 AC: 1207 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3472

East Asian (EAS) AF: 0.0578 AC: 299 AN: 5174

South Asian (SAS) AF: 0.140 AC: 678 AN: 4828

European-Finnish (FIN) AF: 0.0896 AC: 950 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9026 AN: 67998

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.117 Hom.: 1668

Bravo AF: 0.0859

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.70
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs3853241; hg19: chr5-166379772;