4-99366726-C-T

Variant names:

• chr4-99366726-C-T
• rs1583973

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 0.0818 in 152,144 control chromosomes in the GnomAD database, including 612 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 0.082 (612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0818 AC: 12443 AN: 152026 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0495

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0724

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

GnomAD4 genome AF: 0.0818 AC: 12450 AN: 152144 Hom.: 612 Cov.: 32 AF XY: 0.0838 AC XY: 6235 AN XY: 74376

African (AFR) AF: 0.0277 AC: 1149 AN: 41530

American (AMR) AF: 0.0949 AC: 1450 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0495 AC: 172 AN: 3472

East Asian (EAS) AF: 0.0598 AC: 309 AN: 5168

South Asian (SAS) AF: 0.101 AC: 488 AN: 4814

European-Finnish (FIN) AF: 0.144 AC: 1523 AN: 10584

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7155 AN: 67988

Other (OTH) AF: 0.0769 AC: 162 AN: 2108

Alfa AF: 0.0572 Hom.: 68

Bravo AF: 0.0763

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1583973; hg19: chr4-100287883; COSMIC: COSV107199796;