rs4470690

chr4-187800358-C-Achr4-187800358-C-Gchr4-187800358-C-T

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 0.718 in 152,082 control chromosomes in the GnomAD database, including 39,498 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 0.72 (39498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.718 AC: 109110 AN: 151964 Hom.: 39454 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.718 AC: 109209 AN: 152082 Hom.: 39498 Cov.: 32 AF XY: 0.725 AC XY: 53904 AN XY: 74340

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.709

Alfa AF: 0.706 Hom.: 34326

Bravo AF: 0.716

Asia WGS AF: 0.820 AC: 2855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	0.28
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4470690; hg19: chr4-188721512;