rs11729799

Variant names:

• chr4-96149638-C-T
• rs11729799

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 0.362 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.257 AC: 10613 AN: 41354

American (AMR) AF: 0.307 AC: 4676 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5170

South Asian (SAS) AF: 0.301 AC: 1448 AN: 4814

European-Finnish (FIN) AF: 0.470 AC: 4893 AN: 10402

Middle Eastern (MID) AF: 0.344 AC: 99 AN: 288

European-Non Finnish (NFE) AF: 0.434 AC: 29492 AN: 67934

Other (OTH) AF: 0.358 AC: 754 AN: 2106

Alfa AF: 0.402 Hom.: 17692

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs11729799; hg19: chr4-97070789;