4-33716198-T-C

Variant names:

• chr4-33716198-T-C
• rs1444377

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 0.196 in 152,084 control chromosomes in the GnomAD database, including 4,165 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 0.20 (4165 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.16
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 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: 0.196 AC: 29754 AN: 151966 Hom.: 4157 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.196 AC: 29794 AN: 152084 Hom.: 4165 Cov.: 32 AF XY: 0.199 AC XY: 14829 AN XY: 74352

African (AFR) AF: 0.374 AC: 15500 AN: 41428

American (AMR) AF: 0.210 AC: 3204 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1705 AN: 5158

South Asian (SAS) AF: 0.161 AC: 774 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1208 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0954 AC: 6486 AN: 68006

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.134 Hom.: 734

Bravo AF: 0.209

Asia WGS AF: 0.293 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		4.2

Splicing

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

Other links and lift over

dbSNP: rs1444377; hg19: chr4-33717820;