3-110061464-A-T

Variant names:

• chr3-110061464-A-T
• rs2692657

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 0.0825 in 152,210 control chromosomes in the GnomAD database, including 1,080 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 0.082 (1080 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12523 AN: 152092 Hom.: 1073 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0825 AC: 12557 AN: 152210 Hom.: 1080 Cov.: 32 AF XY: 0.0798 AC XY: 5939 AN XY: 74432

African (AFR) AF: 0.223 AC: 9238 AN: 41492

American (AMR) AF: 0.0379 AC: 579 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3472

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5182

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4824

European-Finnish (FIN) AF: 0.0454 AC: 482 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1887 AN: 68028

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0115 Hom.: 7

Bravo AF: 0.0869

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2692657; hg19: chr3-109780311;