chr4-99408536-A-T

Position:

• chr4-99408536-A-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 0.462 in 151,898 control chromosomes in the GnomAD database, including 17,478 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 0.46 (17478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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: 0.462 AC: 70084 AN: 151780 Hom.: 17467 Cov.: 31

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.462 AC: 70140 AN: 151898 Hom.: 17478 Cov.: 31 AF XY: 0.460 AC XY: 34165 AN XY: 74232

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.427

Alfa AF: 0.248 Hom.: 534

Bravo AF: 0.472

Asia WGS AF: 0.470 AC: 1631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969804; hg19: chr4-100329693;