rs1811063

Variant names:

• chr22-15554600-A-G
• rs1811063
• ENST00000412729.1:n.173-3846A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000775240.1(ENSG00000300957):​n.177-3850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.27 (0 hom., cov: 15)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000300957 ENST00000775240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 1 publications found

Genes affected

ENSG00000237299 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775240.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237299	ENST00000412729.1	TSL:6	n.173-3846A>G		intron	N/A
	ENSG00000300957	ENST00000775240.1		n.177-3850A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 21045 AN: 77830 Hom.: 0 Cov.: 15

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.284

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.270 AC: 21060 AN: 77904 Hom.: 0 Cov.: 15 AF XY: 0.266 AC XY: 9966 AN XY: 37436

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

African (AFR) AF: 0.313 AC: 7032 AN: 22452

American (AMR) AF: 0.255 AC: 1993 AN: 7830

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 482 AN: 1822

East Asian (EAS) AF: 0.227 AC: 593 AN: 2608

South Asian (SAS) AF: 0.275 AC: 500 AN: 1820

European-Finnish (FIN) AF: 0.253 AC: 1204 AN: 4758

Middle Eastern (MID) AF: 0.325 AC: 54 AN: 166

European-Non Finnish (NFE) AF: 0.250 AC: 8743 AN: 34908

Other (OTH) AF: 0.283 AC: 304 AN: 1074

⚠️ 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: 0.257 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.7
DANN	Benign	0.22
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1811063; hg19: chr14-19404023; COSMIC: COSV69763622;