rs17088296

Variant names:

• chr4-67350255-G-T
• rs17088296

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 0.0463 in 152,308 control chromosomes in the GnomAD database, including 232 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 0.046 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0664 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: 0.0464 AC: 7062 AN: 152190 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0463 AC: 7057 AN: 152308 Hom.: 232 Cov.: 32 AF XY: 0.0451 AC XY: 3362 AN XY: 74464

African (AFR) AF: 0.0116 AC: 482 AN: 41574

American (AMR) AF: 0.0329 AC: 503 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3470

East Asian (EAS) AF: 0.0563 AC: 292 AN: 5186

South Asian (SAS) AF: 0.0639 AC: 308 AN: 4820

European-Finnish (FIN) AF: 0.0358 AC: 380 AN: 10616

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4627 AN: 68014

Other (OTH) AF: 0.0491 AC: 104 AN: 2116

Alfa AF: 0.0633 Hom.: 153

Bravo AF: 0.0450

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.32
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs17088296; hg19: chr4-68215973; COSMIC: COSV107199599;