chr4-99785875-T-C

Position:

• chr4-99785875-T-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 0.894 in 152,242 control chromosomes in the GnomAD database, including 61,346 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 0.89 (61346 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 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: 0.894 AC: 136044 AN: 152124 Hom.: 61277 Cov.: 33

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.894 AC: 136180 AN: 152242 Hom.: 61346 Cov.: 33 AF XY: 0.889 AC XY: 66190 AN XY: 74436

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.934

Alfa AF: 0.862 Hom.: 2701

Bravo AF: 0.901

Asia WGS AF: 0.684 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1078636; hg19: chr4-100707032;