rs11930528

Variant names:

• chr4-110739038-G-T
• rs11930528

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 0.206 in 152,072 control chromosomes in the GnomAD database, including 3,879 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 0.21 (3879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.206 AC: 31242 AN: 151954 Hom.: 3862 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.206 AC: 31298 AN: 152072 Hom.: 3879 Cov.: 32 AF XY: 0.212 AC XY: 15786 AN XY: 74334

African (AFR) AF: 0.292 AC: 12098 AN: 41464

American (AMR) AF: 0.230 AC: 3509 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2273 AN: 5158

South Asian (SAS) AF: 0.198 AC: 953 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1598 AN: 10574

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9161 AN: 67988

Other (OTH) AF: 0.211 AC: 447 AN: 2116

Alfa AF: 0.174 Hom.: 2058

Bravo AF: 0.216

Asia WGS AF: 0.288 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.55
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11930528; hg19: chr4-111660194;