chr4-99070525-C-T

Position:

• chr4-99070525-C-T

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 0.0814 in 152,298 control chromosomes in the GnomAD database, including 540 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 0.081 (540 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.99070525C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12388 AN: 152180 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.0732

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.0814 AC: 12396 AN: 152298 Hom.: 540 Cov.: 32 AF XY: 0.0767 AC XY: 5711 AN XY: 74470

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.0849

Gnomad4 ASJ AF: 0.0861

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0447

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0974

Alfa AF: 0.0911 Hom.: 257

Bravo AF: 0.0850

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7684986; hg19: chr4-99991676;