rs4440177

chr4-162321901-G-A

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 0.448 in 151,922 control chromosomes in the GnomAD database, including 17,120 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 0.45 (17120 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.448 AC: 67993 AN: 151802 Hom.: 17071 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.448 AC: 68112 AN: 151922 Hom.: 17120 Cov.: 32 AF XY: 0.444 AC XY: 32958 AN XY: 74234

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.439

Alfa AF: 0.375 Hom.: 16204

Bravo AF: 0.472

Asia WGS AF: 0.429 AC: 1492 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4440177; hg19: chr4-163243053;