rs17407555

Variant names:

• chr4-10273370-A-G
• rs17407555

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 0.178 in 152,198 control chromosomes in the GnomAD database, including 2,817 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 0.18 (2817 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.178 AC: 27136 AN: 152080 Hom.: 2816 Cov.: 33

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.178 AC: 27132 AN: 152198 Hom.: 2817 Cov.: 33 AF XY: 0.177 AC XY: 13164 AN XY: 74390

African (AFR) AF: 0.0905 AC: 3761 AN: 41540

American (AMR) AF: 0.126 AC: 1922 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.160 AC: 828 AN: 5184

South Asian (SAS) AF: 0.136 AC: 654 AN: 4818

European-Finnish (FIN) AF: 0.239 AC: 2528 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16269 AN: 67994

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.198 Hom.: 1471

Bravo AF: 0.165

Asia WGS AF: 0.153 AC: 533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.28
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs17407555; hg19: chr4-10274994;