rs17051145

Variant names:

• chr4-120623983-T-G
• rs17051145

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 0.197 in 152,132 control chromosomes in the GnomAD database, including 3,638 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 0.20 (3638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.197 AC: 29908 AN: 152014 Hom.: 3634 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.197 AC: 29954 AN: 152132 Hom.: 3638 Cov.: 32 AF XY: 0.198 AC XY: 14704 AN XY: 74380

African (AFR) AF: 0.334 AC: 13828 AN: 41460

American (AMR) AF: 0.119 AC: 1823 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 308 AN: 3468

East Asian (EAS) AF: 0.103 AC: 536 AN: 5182

South Asian (SAS) AF: 0.234 AC: 1128 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1898 AN: 10600

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9828 AN: 68008

Other (OTH) AF: 0.173 AC: 365 AN: 2108

Alfa AF: 0.153 Hom.: 3573

Bravo AF: 0.194

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs17051145; hg19: chr4-121545138;