4-99363528-A-T

Variant names:

• chr4-99363528-A-T
• rs1229849

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 0.232 in 152,028 control chromosomes in the GnomAD database, including 4,831 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 0.23 (4831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 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: 0.232 AC: 35216 AN: 151910 Hom.: 4828 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.232 AC: 35229 AN: 152028 Hom.: 4831 Cov.: 32 AF XY: 0.230 AC XY: 17105 AN XY: 74286

African (AFR) AF: 0.116 AC: 4823 AN: 41480

American (AMR) AF: 0.198 AC: 3029 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5178

South Asian (SAS) AF: 0.205 AC: 987 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3904 AN: 10552

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20872 AN: 67946

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.276 Hom.: 795

Bravo AF: 0.212

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs1229849; hg19: chr4-100284685;