4-99406507-C-T

Variant names:

• chr4-99406507-C-T
• rs994772

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 0.131 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.131 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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.136

Alfa AF: 0.115 Hom.: 633

Bravo AF: 0.129

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994772; hg19: chr4-100327664;