4-99739429-C-T

Variant names:

• chr4-99739429-C-T
• rs752766

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 0.346 in 152,116 control chromosomes in the GnomAD database, including 10,952 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 0.35 (10952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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: 0.345 AC: 52498 AN: 151998 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.346 AC: 52604 AN: 152116 Hom.: 10952 Cov.: 32 AF XY: 0.337 AC XY: 25065 AN XY: 74382

African (AFR) AF: 0.579 AC: 24000 AN: 41466

American (AMR) AF: 0.328 AC: 5013 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1080 AN: 5180

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4824

European-Finnish (FIN) AF: 0.132 AC: 1402 AN: 10598

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17907 AN: 67990

Other (OTH) AF: 0.333 AC: 701 AN: 2106

Alfa AF: 0.305 Hom.: 1022

Bravo AF: 0.369

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.62
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs752766; hg19: chr4-100660586;