rs1484322

chr4-39669522-G-Achr4-39669522-G-Cchr4-39669522-G-T

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 0.3 in 151,994 control chromosomes in the GnomAD database, including 8,157 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 0.30 (8157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45557 AN: 151876 Hom.: 8146 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.300 AC: 45575 AN: 151994 Hom.: 8157 Cov.: 32 AF XY: 0.298 AC XY: 22126 AN XY: 74286

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.353

Alfa AF: 0.361 Hom.: 17665

Bravo AF: 0.304

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	11
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1484322; hg19: chr4-39671142;