ENST00000730429.1:n.264+52642A>G

Variant names:

• chr11-35865369-T-C
• rs684909
• ENST00000730429.1:n.264+52642A>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+52642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,070 control chromosomes in the GnomAD database, including 25,209 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 0.57 (25209 hom., cov: 32)
• Consequence: ENSG00000254919 ENST00000730429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.632 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+52642A>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730430.1	n.268+52642A>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730431.1	n.265+52642A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86494 AN: 151952 Hom.: 25200 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.569 AC: 86548 AN: 152070 Hom.: 25209 Cov.: 32 AF XY: 0.572 AC XY: 42555 AN XY: 74334

African (AFR) AF: 0.446 AC: 18532 AN: 41506

American (AMR) AF: 0.642 AC: 9819 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3203 AN: 5148

South Asian (SAS) AF: 0.536 AC: 2579 AN: 4814

European-Finnish (FIN) AF: 0.682 AC: 7212 AN: 10576

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41346 AN: 67958

Other (OTH) AF: 0.557 AC: 1175 AN: 2110

Alfa AF: 0.596 Hom.: 54931

Bravo AF: 0.562

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.83
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs684909; hg19: chr11-35886919; COSMIC: COSV73331315;