11-94880589-A-G

Variant names:

• chr11-94880589-A-G
• rs690309
• ENST00000545958.1:n.98-6042T>C

Variant summary

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

The ENST00000545958.1(ENSG00000256469):​n.98-6042T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,284 control chromosomes in the GnomAD database, including 64,455 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 0.91 (64455 hom., cov: 32)
• Consequence: ENSG00000256469 ENST00000545958.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 2 publications found

Genes affected

ENSG00000256469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 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
ENSG00000256469	ENST00000545958.1	n.98-6042T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138968 AN: 152166 Hom.: 64424 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.913 AC: 139052 AN: 152284 Hom.: 64455 Cov.: 32 AF XY: 0.915 AC XY: 68165 AN XY: 74478

African (AFR) AF: 0.732 AC: 30379 AN: 41508

American (AMR) AF: 0.953 AC: 14595 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3397 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5193 AN: 5194

South Asian (SAS) AF: 0.997 AC: 4815 AN: 4830

European-Finnish (FIN) AF: 0.977 AC: 10372 AN: 10618

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67153 AN: 68038

Other (OTH) AF: 0.924 AC: 1951 AN: 2112

Alfa AF: 0.969 Hom.: 33624

Bravo AF: 0.904

Asia WGS AF: 0.985 AC: 3426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.77
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs690309; hg19: chr11-94613754;