rs4690464

Variant names:

• chr4-176819431-G-A
• rs4690464

Your query was ambiguous. Multiple possible variants found:

• chr4-176819431-G-A
• chr4-176819431-G-C

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 0.675 in 151,958 control chromosomes in the GnomAD database, including 39,127 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 0.67 (39127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.675 AC: 102521 AN: 151840 Hom.: 39121 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.675 AC: 102548 AN: 151958 Hom.: 39127 Cov.: 33 AF XY: 0.681 AC XY: 50530 AN XY: 74254

African (AFR) AF: 0.287 AC: 11890 AN: 41470

American (AMR) AF: 0.760 AC: 11606 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2977 AN: 3464

East Asian (EAS) AF: 0.987 AC: 5112 AN: 5180

South Asian (SAS) AF: 0.807 AC: 3892 AN: 4822

European-Finnish (FIN) AF: 0.814 AC: 8567 AN: 10526

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55901 AN: 67908

Other (OTH) AF: 0.731 AC: 1545 AN: 2114

Alfa AF: 0.786 Hom.: 24782

Bravo AF: 0.655

Asia WGS AF: 0.857 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4690464; hg19: chr4-177740585;