17-34285383-C-T

Variant names:

• chr17-34285383-C-T
• rs16969415

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 0.0428 in 152,058 control chromosomes in the GnomAD database, including 274 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 0.043 (274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 22 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 (SAS) allele frequency at 95% confidence interval = 0.203 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: 0.0428 AC: 6496 AN: 151942 Hom.: 271 Cov.: 31

Gnomad AFR AF: 0.00955

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0415

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0428 AC: 6506 AN: 152058 Hom.: 274 Cov.: 31 AF XY: 0.0463 AC XY: 3444 AN XY: 74334

African (AFR) AF: 0.00952 AC: 395 AN: 41486

American (AMR) AF: 0.0414 AC: 632 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.0897 AC: 462 AN: 5152

South Asian (SAS) AF: 0.213 AC: 1022 AN: 4790

European-Finnish (FIN) AF: 0.0530 AC: 561 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3088 AN: 67972

Other (OTH) AF: 0.0508 AC: 107 AN: 2106

Alfa AF: 0.0396 Hom.: 130

Bravo AF: 0.0366

Asia WGS AF: 0.160 AC: 554 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	0.33
DANN	Benign	0.48
PhyloP100		-2.2
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs16969415; hg19: chr17-32612402;