4-99406180-T-G

Position:

• chr4-99406180-T-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 0.358 in 147,932 control chromosomes in the GnomAD database, including 9,715 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 0.36 (9715 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.99406180T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.358 AC: 52891 AN: 147850 Hom.: 9711 Cov.: 30

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.358 AC: 52924 AN: 147932 Hom.: 9715 Cov.: 30 AF XY: 0.361 AC XY: 25961 AN XY: 71974

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.357

Alfa AF: 0.214 Hom.: 502

Bravo AF: 0.343

Asia WGS AF: 0.448 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2083687; hg19: chr4-100327337;