4-161329780-A-G

Variant names:

• chr4-161329780-A-G
• rs4470583

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 0.956 in 152,008 control chromosomes in the GnomAD database, including 69,726 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 0.96 (69726 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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: 0.956 AC: 145238 AN: 151890 Hom.: 69675 Cov.: 29

Gnomad AFR AF: 0.865

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.951

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.956 AC: 145349 AN: 152008 Hom.: 69726 Cov.: 29 AF XY: 0.956 AC XY: 71047 AN XY: 74304

African (AFR) AF: 0.865 AC: 35848 AN: 41420

American (AMR) AF: 0.979 AC: 14927 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3459 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4782 AN: 5130

South Asian (SAS) AF: 0.951 AC: 4578 AN: 4814

European-Finnish (FIN) AF: 1.00 AC: 10595 AN: 10596

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67926 AN: 68016

Other (OTH) AF: 0.964 AC: 2035 AN: 2112

Alfa AF: 0.982 Hom.: 216911

Bravo AF: 0.950

Asia WGS AF: 0.952 AC: 3308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.47
DANN	Benign	0.41
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4470583; hg19: chr4-162250932;