rs4440177

Variant names:

• chr4-162321901-G-A
• rs4440177

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 0.448 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.684 AC: 28350 AN: 41448

American (AMR) AF: 0.408 AC: 6224 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2337 AN: 5162

South Asian (SAS) AF: 0.420 AC: 2027 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2811 AN: 10532

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23182 AN: 67914

Other (OTH) AF: 0.439 AC: 925 AN: 2108

Alfa AF: 0.378 Hom.: 23241

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4440177; hg19: chr4-163243053;