rs11728154

Variant names:

• chr4-148739571-G-A
• rs11728154
• ENST00000661928.1:n.223-127186G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661928.1(ENSG00000287292):​n.223-127186G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,156 control chromosomes in the GnomAD database, including 1,752 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 0.14 (1752 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 2 publications found

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3662-127186G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.223-127186G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20686 AN: 152038 Hom.: 1754 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.136 AC: 20679 AN: 152156 Hom.: 1752 Cov.: 32 AF XY: 0.133 AC XY: 9889 AN XY: 74386

African (AFR) AF: 0.0561 AC: 2331 AN: 41522

American (AMR) AF: 0.122 AC: 1870 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3472

East Asian (EAS) AF: 0.0624 AC: 323 AN: 5180

South Asian (SAS) AF: 0.149 AC: 716 AN: 4820

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10570

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13152 AN: 67986

Other (OTH) AF: 0.148 AC: 312 AN: 2108

Alfa AF: 0.169 Hom.: 837

Bravo AF: 0.133

Asia WGS AF: 0.0920 AC: 321 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.094
DANN	Benign	0.46
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs11728154; hg19: chr4-149660723;