rs4077566

Variant names:

• chr11-124901375-A-G
• rs4077566
• ENST00000524433.2:n.483+9243A>G

Variant summary

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

The ENST00000524433.2(ENSG00000254943):​n.483+9243A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,850 control chromosomes in the GnomAD database, including 6,956 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 0.27 (6956 hom., cov: 31)
• Consequence: ENSG00000254943 ENST00000524433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 8 publications found

Genes affected

ENSG00000254943 (HGNC:):

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 = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984406	XR_001748429.3	n.334+9243A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254943	ENST00000524433.2	n.483+9243A>G		intron_variant	Intron 2 of 2	4
ENSG00000254943	ENST00000828696.1	n.328+9243A>G		intron_variant	Intron 2 of 2
ENSG00000254943	ENST00000828697.1	n.278+9243A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41355 AN: 151730 Hom.: 6964 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.272 AC: 41336 AN: 151850 Hom.: 6956 Cov.: 31 AF XY: 0.265 AC XY: 19647 AN XY: 74226

African (AFR) AF: 0.110 AC: 4546 AN: 41406

American (AMR) AF: 0.232 AC: 3542 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5176

South Asian (SAS) AF: 0.129 AC: 619 AN: 4788

European-Finnish (FIN) AF: 0.353 AC: 3716 AN: 10532

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.396 AC: 26869 AN: 67912

Other (OTH) AF: 0.287 AC: 605 AN: 2108

Alfa AF: 0.333 Hom.: 17781

Bravo AF: 0.257

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4077566; hg19: chr11-124771271;