4-99406507-C-T

Variant names:

• chr4-99406507-C-T
• rs994772

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.131 in 152,082 control chromosomes in the GnomAD database, including 1,465 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 0.13 (1465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19869 AN: 151962 Hom.: 1463 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.131 AC: 19882 AN: 152082 Hom.: 1465 Cov.: 32 AF XY: 0.137 AC XY: 10221 AN XY: 74350

African (AFR) AF: 0.112 AC: 4637 AN: 41490

American (AMR) AF: 0.207 AC: 3158 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5172

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10574

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7254 AN: 67992

Other (OTH) AF: 0.136 AC: 287 AN: 2106

Alfa AF: 0.112 Hom.: 2051

Bravo AF: 0.129

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.70
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs994772; hg19: chr4-100327664;