rs11732323

Variant names:

• chr4-54776950-G-A
• rs11732323
• ENST00000821119.1:n.439+1351G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-54776950-G-A
• chr4-54776950-G-T

Variant summary

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

The ENST00000821119.1(ENSG00000306785):​n.439+1351G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,106 control chromosomes in the GnomAD database, including 2,266 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 0.17 (2266 hom., cov: 32)
• Consequence: ENSG00000306785 ENST00000821119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 4 publications found

Genes affected

ENSG00000306785 (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 (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377657	XR_941053.3	n.360+1262G>A		intron_variant	Intron 2 of 2
LOC105377657	XR_941054.3	n.818+1262G>A		intron_variant	Intron 2 of 2
LOC105377657	XR_941055.3	n.360+1262G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306785	ENST00000821119.1	n.439+1351G>A		intron_variant	Intron 2 of 3
ENSG00000306785	ENST00000821120.1	n.677+1262G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25214 AN: 151988 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.166 AC: 25214 AN: 152106 Hom.: 2266 Cov.: 32 AF XY: 0.168 AC XY: 12497 AN XY: 74350

African (AFR) AF: 0.152 AC: 6311 AN: 41494

American (AMR) AF: 0.118 AC: 1808 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 311 AN: 3468

East Asian (EAS) AF: 0.296 AC: 1528 AN: 5160

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10568

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11475 AN: 67988

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.163 Hom.: 9091

Bravo AF: 0.160

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs11732323; hg19: chr4-55643116;