rs73229797

Variant names:

• chr4-40334646-A-G
• rs73229797

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 0.179 in 152,068 control chromosomes in the GnomAD database, including 2,924 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 0.18 (2924 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 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: 0.180 AC: 27284 AN: 151950 Hom.: 2926 Cov.: 31

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.179 AC: 27286 AN: 152068 Hom.: 2924 Cov.: 31 AF XY: 0.179 AC XY: 13280 AN XY: 74342

African (AFR) AF: 0.0732 AC: 3040 AN: 41522

American (AMR) AF: 0.177 AC: 2702 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3468

East Asian (EAS) AF: 0.0531 AC: 275 AN: 5178

South Asian (SAS) AF: 0.149 AC: 715 AN: 4810

European-Finnish (FIN) AF: 0.246 AC: 2599 AN: 10544

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16847 AN: 67960

Other (OTH) AF: 0.183 AC: 385 AN: 2106

Alfa AF: 0.212 Hom.: 487

Bravo AF: 0.168

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.64
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs73229797; hg19: chr4-40336663;