chr4-96149638-C-T

Variant names:

• chr4-96149638-C-T
• rs11729799

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.362 in 151,672 control chromosomes in the GnomAD database, including 10,566 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 0.36 (10566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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: 0.362 AC: 54867 AN: 151562 Hom.: 10568 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.362 AC: 54874 AN: 151672 Hom.: 10566 Cov.: 32 AF XY: 0.359 AC XY: 26617 AN XY: 74108

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.358

Alfa AF: 0.391 Hom.: 2929

Bravo AF: 0.346

Asia WGS AF: 0.238 AC: 828 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11729799; hg19: chr4-97070789;