rs578169

Variant names:

• chr11-104990916-A-C
• rs578169
• ENST00000797905.1:n.566-13915A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-104990916-A-C
• chr11-104990916-A-G

Variant summary

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

The ENST00000797905.1(ENSG00000303891):​n.566-13915A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,972 control chromosomes in the GnomAD database, including 25,945 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 0.58 (25945 hom., cov: 32)
• Consequence: ENSG00000303891 ENST00000797905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

ENSG00000303891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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
ENSG00000303891	ENST00000797905.1	n.566-13915A>C		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88200 AN: 151856 Hom.: 25931 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.581 AC: 88250 AN: 151972 Hom.: 25945 Cov.: 32 AF XY: 0.582 AC XY: 43252 AN XY: 74286

African (AFR) AF: 0.605 AC: 25069 AN: 41470

American (AMR) AF: 0.497 AC: 7591 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2326 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3986 AN: 5156

South Asian (SAS) AF: 0.608 AC: 2924 AN: 4808

European-Finnish (FIN) AF: 0.582 AC: 6155 AN: 10580

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38136 AN: 67914

Other (OTH) AF: 0.608 AC: 1283 AN: 2110

Alfa AF: 0.570 Hom.: 3690

Bravo AF: 0.577

Asia WGS AF: 0.685 AC: 2376 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.66
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs578169; hg19: chr11-104861643;