rs4574216

Variant names:

• chr3-149441969-A-C
• rs4574216

Your query was ambiguous. Multiple possible variants found:

• chr3-149441969-A-C
• chr3-149441969-A-T

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 0.934 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.971 AC: 40373 AN: 41570

American (AMR) AF: 0.953 AC: 14581 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3004 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3934 AN: 5182

South Asian (SAS) AF: 0.884 AC: 4266 AN: 4828

European-Finnish (FIN) AF: 0.927 AC: 9836 AN: 10614

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63160 AN: 68020

Other (OTH) AF: 0.934 AC: 1975 AN: 2114

Alfa AF: 0.935 Hom.: 9798

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4574216; hg19: chr3-149159756;