4-99446634-C-T

Variant names:

• chr4-99446634-C-T
• rs749407

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 0.318 in 151,776 control chromosomes in the GnomAD database, including 8,546 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 0.32 (8546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 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: 0.318 AC: 48291 AN: 151656 Hom.: 8543 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.318 AC: 48314 AN: 151776 Hom.: 8546 Cov.: 32 AF XY: 0.321 AC XY: 23809 AN XY: 74162

African (AFR) AF: 0.167 AC: 6899 AN: 41416

American (AMR) AF: 0.395 AC: 6024 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1376 AN: 5156

South Asian (SAS) AF: 0.316 AC: 1520 AN: 4808

European-Finnish (FIN) AF: 0.393 AC: 4139 AN: 10544

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26349 AN: 67842

Other (OTH) AF: 0.315 AC: 663 AN: 2104

Alfa AF: 0.198 Hom.: 464

Bravo AF: 0.316

Asia WGS AF: 0.323 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.66
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs749407; hg19: chr4-100367791;