rs1163091

Variant names:

• chr4-49569822-C-G
• rs1163091
• ENST00000726615.1:n.309+12413C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-49569822-C-G
• chr4-49569822-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000726615.1(ENSG00000294903):​n.309+12413C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 137,864 control chromosomes in the GnomAD database, including 7 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 0.013 (7 hom., cov: 51)
• Consequence: ENSG00000294903 ENST00000726615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87
• Publications: 1 publications found

Genes affected

ENSG00000294903 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 7 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726615.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294903	ENST00000726615.1		n.309+12413C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0127 AC: 1749 AN: 137816 Hom.: 6 Cov.: 51

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00561

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000969

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00787

Gnomad NFE AF: 0.000166

Gnomad OTH AF: 0.00839

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

GnomAD4 genome AF: 0.0127 AC: 1757 AN: 137864 Hom.: 7 Cov.: 51 AF XY: 0.0122 AC XY: 813 AN XY: 66390

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0476 AC: 1651 AN: 34704

American (AMR) AF: 0.00561 AC: 73 AN: 13018

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3398

East Asian (EAS) AF: 0.00 AC: 0 AN: 4654

South Asian (SAS) AF: 0.000971 AC: 4 AN: 4118

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8712

Middle Eastern (MID) AF: 0.00840 AC: 2 AN: 238

European-Non Finnish (NFE) AF: 0.000166 AC: 11 AN: 66222

Other (OTH) AF: 0.00832 AC: 16 AN: 1922

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.5
DANN	Benign	0.32
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs1163091; hg19: chr4-49571839;