chr3-19741785-T-C

Variant names:

• chr3-19741785-T-C
• rs17006217

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 0.158 in 151,138 control chromosomes in the GnomAD database, including 2,005 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 0.16 (2005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 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: 0.158 AC: 23786 AN: 151020 Hom.: 1992 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.158 AC: 23832 AN: 151138 Hom.: 2005 Cov.: 32 AF XY: 0.159 AC XY: 11784 AN XY: 73912

African (AFR) AF: 0.224 AC: 9222 AN: 41164

American (AMR) AF: 0.130 AC: 1981 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 280 AN: 3444

East Asian (EAS) AF: 0.178 AC: 909 AN: 5116

South Asian (SAS) AF: 0.225 AC: 1071 AN: 4750

European-Finnish (FIN) AF: 0.124 AC: 1303 AN: 10548

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.127 AC: 8590 AN: 67626

Other (OTH) AF: 0.154 AC: 323 AN: 2092

Alfa AF: 0.135 Hom.: 4140

Bravo AF: 0.156

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs17006217; hg19: chr3-19783277;