rs17007301

Variant names:

• chr4-141488826-G-A
• rs17007301

Your query was ambiguous. Multiple possible variants found:

• chr4-141488826-G-A
• chr4-141488826-G-C

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 0.221 in 152,112 control chromosomes in the GnomAD database, including 4,021 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 0.22 (4021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.221 AC: 33574 AN: 151994 Hom.: 4003 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.221 AC: 33644 AN: 152112 Hom.: 4021 Cov.: 32 AF XY: 0.220 AC XY: 16380 AN XY: 74358

African (AFR) AF: 0.304 AC: 12616 AN: 41470

American (AMR) AF: 0.268 AC: 4092 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1130 AN: 5176

South Asian (SAS) AF: 0.190 AC: 917 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10584

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12313 AN: 68004

Other (OTH) AF: 0.210 AC: 444 AN: 2110

Alfa AF: 0.210 Hom.: 1337

Bravo AF: 0.234

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.21
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs17007301; hg19: chr4-142409979;