rs4605724

Variant names:

• chr4-110763925-C-A
• rs4605724

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 0.148 in 152,210 control chromosomes in the GnomAD database, including 2,072 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 0.15 (2072 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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: 0.148 AC: 22466 AN: 152092 Hom.: 2070 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.148 AC: 22484 AN: 152210 Hom.: 2072 Cov.: 33 AF XY: 0.154 AC XY: 11460 AN XY: 74428

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.156

Alfa AF: 0.135 Hom.: 2764

Bravo AF: 0.150

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.9
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: rs4605724; hg19: chr4-111685081;