rs7668417

Variant names:

• chr4-18023406-G-A
• rs7668417

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.238 in 152,174 control chromosomes in the GnomAD database, including 5,485 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 0.24 (5485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.237 AC: 36078 AN: 152056 Hom.: 5453 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.238 AC: 36151 AN: 152174 Hom.: 5485 Cov.: 33 AF XY: 0.233 AC XY: 17355 AN XY: 74404

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.0915

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.234

Alfa AF: 0.182 Hom.: 813

Bravo AF: 0.251

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7668417; hg19: chr4-18025029;