chr4-99785875-T-C

Variant names:

• chr4-99785875-T-C
• rs1078636

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;