3-186840168-T-C

Variant names:

• chr3-186840168-T-C
• rs860291

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 0.908 in 152,236 control chromosomes in the GnomAD database, including 62,949 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 (62949 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 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: 0.908 AC: 138146 AN: 152118 Hom.: 62886 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.908 AC: 138270 AN: 152236 Hom.: 62949 Cov.: 31 AF XY: 0.910 AC XY: 67678 AN XY: 74410

African (AFR) AF: 0.970 AC: 40287 AN: 41546

American (AMR) AF: 0.894 AC: 13677 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3111 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4677 AN: 5176

South Asian (SAS) AF: 0.847 AC: 4085 AN: 4822

European-Finnish (FIN) AF: 0.944 AC: 9997 AN: 10594

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59393 AN: 68010

Other (OTH) AF: 0.905 AC: 1912 AN: 2112

Alfa AF: 0.889 Hom.: 20556

Bravo AF: 0.907

Asia WGS AF: 0.905 AC: 3146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs860291; hg19: chr3-186557957;