rs4599440

Variant names:

• chr4-61100555-T-C
• rs4599440

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 0.679 in 152,108 control chromosomes in the GnomAD database, including 36,474 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 0.68 (36474 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103325 AN: 151990 Hom.: 36477 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.679 AC: 103348 AN: 152108 Hom.: 36474 Cov.: 33 AF XY: 0.675 AC XY: 50190 AN XY: 74334

African (AFR) AF: 0.505 AC: 20946 AN: 41462

American (AMR) AF: 0.799 AC: 12206 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2563 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2082 AN: 5170

South Asian (SAS) AF: 0.560 AC: 2700 AN: 4818

European-Finnish (FIN) AF: 0.704 AC: 7449 AN: 10584

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53046 AN: 68006

Other (OTH) AF: 0.695 AC: 1467 AN: 2110

Alfa AF: 0.744 Hom.: 196865

Bravo AF: 0.679

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs4599440; hg19: chr4-61966273;