4-73990141-A-G

Variant names:

• chr4-73990141-A-G
• rs552582

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 0.792 in 152,074 control chromosomes in the GnomAD database, including 49,863 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 0.79 (49863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.793 AC: 120458 AN: 151956 Hom.: 49867 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.792 AC: 120479 AN: 152074 Hom.: 49863 Cov.: 32 AF XY: 0.797 AC XY: 59267 AN XY: 74362

African (AFR) AF: 0.523 AC: 21677 AN: 41416

American (AMR) AF: 0.894 AC: 13663 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3040 AN: 3470

East Asian (EAS) AF: 0.966 AC: 4992 AN: 5170

South Asian (SAS) AF: 0.894 AC: 4320 AN: 4830

European-Finnish (FIN) AF: 0.883 AC: 9375 AN: 10614

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60553 AN: 67972

Other (OTH) AF: 0.812 AC: 1715 AN: 2112

Alfa AF: 0.808 Hom.: 9872

Bravo AF: 0.780

Asia WGS AF: 0.863 AC: 2998 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	1.1
DANN	Benign	0.17
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs552582; hg19: chr4-74855858;