chr3-69645755-C-T

Variant names:

• chr3-69645755-C-T
• rs17006293

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 0.0472 in 152,230 control chromosomes in the GnomAD database, including 372 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 0.047 (372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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: 0.0472 AC: 7176 AN: 152112 Hom.: 371 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0472 AC: 7184 AN: 152230 Hom.: 372 Cov.: 32 AF XY: 0.0510 AC XY: 3793 AN XY: 74420

African (AFR) AF: 0.0124 AC: 515 AN: 41540

American (AMR) AF: 0.109 AC: 1672 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1279 AN: 5178

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4824

European-Finnish (FIN) AF: 0.0587 AC: 622 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2535 AN: 68022

Other (OTH) AF: 0.0529 AC: 112 AN: 2116

Alfa AF: 0.0445 Hom.: 313

Bravo AF: 0.0512

Asia WGS AF: 0.130 AC: 454 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	2.7
DANN	Benign	0.66
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs17006293; hg19: chr3-69694906;