3-146170670-T-G

Variant names:

• chr3-146170670-T-G
• rs1913185

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 0.153 in 151,956 control chromosomes in the GnomAD database, including 1,907 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 0.15 (1907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.153 AC: 23241 AN: 151838 Hom.: 1904 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.153 AC: 23248 AN: 151956 Hom.: 1907 Cov.: 32 AF XY: 0.153 AC XY: 11370 AN XY: 74298

African (AFR) AF: 0.110 AC: 4553 AN: 41300

American (AMR) AF: 0.198 AC: 3029 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5174

South Asian (SAS) AF: 0.131 AC: 631 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1545 AN: 10610

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11126 AN: 68002

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.167 Hom.: 4195

Bravo AF: 0.157

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.82
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1913185; hg19: chr3-145888457;