rs729147

chr4-99412110-G-Achr4-99412110-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.775 in 151,924 control chromosomes in the GnomAD database, including 46,135 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 0.78 (46135 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117703 AN: 151806 Hom.: 46101 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.775 AC: 117789 AN: 151924 Hom.: 46135 Cov.: 31 AF XY: 0.769 AC XY: 57115 AN XY: 74244

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.728

Alfa AF: 0.778 Hom.: 98615

Bravo AF: 0.764

Asia WGS AF: 0.600 AC: 2086 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.58
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729147; hg19: chr4-100333267;