chr3-172550013-T-C

Variant names:

• chr3-172550013-T-C
• rs13074711

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 0.171 in 152,192 control chromosomes in the GnomAD database, including 2,944 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 0.17 (2944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25906 AN: 152074 Hom.: 2932 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.171 AC: 25954 AN: 152192 Hom.: 2944 Cov.: 32 AF XY: 0.168 AC XY: 12527 AN XY: 74402

African (AFR) AF: 0.316 AC: 13094 AN: 41490

American (AMR) AF: 0.111 AC: 1702 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3468

East Asian (EAS) AF: 0.140 AC: 726 AN: 5182

South Asian (SAS) AF: 0.0566 AC: 273 AN: 4826

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7867 AN: 68024

Other (OTH) AF: 0.150 AC: 316 AN: 2112

Alfa AF: 0.157 Hom.: 1768

Bravo AF: 0.175

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs13074711; hg19: chr3-172267803;