rs4574216

Positions:

• chr3-149441969-A-C
• chr3-149441969-A-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 0.934 in 152,304 control chromosomes in the GnomAD database, including 66,567 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 0.93 (66567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142111 AN: 152186 Hom.: 66510 Cov.: 33

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.934 AC: 142227 AN: 152304 Hom.: 66567 Cov.: 33 AF XY: 0.932 AC XY: 69393 AN XY: 74472

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.934

Alfa AF: 0.933 Hom.: 9429

Bravo AF: 0.940

Asia WGS AF: 0.860 AC: 2989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4574216; hg19: chr3-149159756;