chr4-98732053-A-G

Position:

• chr4-98732053-A-G

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 0.182 in 152,186 control chromosomes in the GnomAD database, including 3,053 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 (3053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.182 AC: 27626 AN: 152066 Hom.: 3033 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.182 AC: 27697 AN: 152186 Hom.: 3053 Cov.: 32 AF XY: 0.186 AC XY: 13858 AN XY: 74408

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.179

Alfa AF: 0.136 Hom.: 929

Bravo AF: 0.188

Asia WGS AF: 0.257 AC: 891 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	0.019
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17028008; hg19: chr4-99653204;