chr11-35872869-G-C

Variant names:

• chr11-35872869-G-C
• rs728749
• ENST00000730429.1:n.264+45142C>G

Variant summary

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

The ENST00000730429.1(ENSG00000254919):​n.264+45142C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,096 control chromosomes in the GnomAD database, including 25,540 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 0.54 (25540 hom., cov: 33)
• Consequence: ENSG00000254919 ENST00000730429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 1 publications found

Genes affected

ENSG00000254919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 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
ENSG00000254919	ENST00000730429.1	n.264+45142C>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730430.1	n.268+45142C>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730431.1	n.265+45142C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81940 AN: 151976 Hom.: 25528 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.539 AC: 81960 AN: 152096 Hom.: 25540 Cov.: 33 AF XY: 0.540 AC XY: 40129 AN XY: 74346

African (AFR) AF: 0.215 AC: 8934 AN: 41484

American (AMR) AF: 0.654 AC: 9983 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2138 AN: 5172

South Asian (SAS) AF: 0.477 AC: 2292 AN: 4810

European-Finnish (FIN) AF: 0.724 AC: 7664 AN: 10592

Middle Eastern (MID) AF: 0.603 AC: 175 AN: 290

European-Non Finnish (NFE) AF: 0.692 AC: 47018 AN: 67988

Other (OTH) AF: 0.556 AC: 1170 AN: 2104

Alfa AF: 0.610 Hom.: 3814

Bravo AF: 0.523

Asia WGS AF: 0.440 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.070
DANN	Benign	0.39
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs728749; hg19: chr11-35894419;