rs17622933

Variant names:

• chr4-24789058-T-A
• rs17622933

Your query was ambiguous. Multiple possible variants found:

• chr4-24789058-T-A
• chr4-24789058-T-C
• chr4-24789058-T-G

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 0.264 in 151,914 control chromosomes in the GnomAD database, including 6,063 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 0.26 (6063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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: 0.264 AC: 40065 AN: 151796 Hom.: 6058 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.264 AC: 40085 AN: 151914 Hom.: 6063 Cov.: 32 AF XY: 0.263 AC XY: 19534 AN XY: 74268

African (AFR) AF: 0.153 AC: 6355 AN: 41428

American (AMR) AF: 0.274 AC: 4175 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2861 AN: 5154

South Asian (SAS) AF: 0.419 AC: 2017 AN: 4812

European-Finnish (FIN) AF: 0.201 AC: 2121 AN: 10538

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20374 AN: 67942

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.144 Hom.: 287

Bravo AF: 0.264

Asia WGS AF: 0.437 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs17622933; hg19: chr4-24790680;