rs4464522

Variant names:

• chr4-31239120-T-C
• rs4464522

Your query was ambiguous. Multiple possible variants found:

• chr4-31239120-T-C
• chr4-31239120-T-G

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 0.417 in 151,864 control chromosomes in the GnomAD database, including 14,463 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 0.42 (14463 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 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: 0.417 AC: 63332 AN: 151746 Hom.: 14431 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.417 AC: 63402 AN: 151864 Hom.: 14463 Cov.: 32 AF XY: 0.416 AC XY: 30848 AN XY: 74236

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.439

Alfa AF: 0.375 Hom.: 1845

Bravo AF: 0.428

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4464522; hg19: chr4-31240742;