rs228173

Variant names:

• chr1-143405602-T-C
• rs228173
• ENST00000721367.1:n.286+14471A>G

Variant summary

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

The ENST00000721367.1(ENSG00000294133):​n.286+14471A>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 0.11 (2 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000294133 ENST00000721367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 1 publications found

Genes affected

ENSG00000294133 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721367.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294133	ENST00000721367.1		n.286+14471A>G		intron	N/A
	ENSG00000294133	ENST00000721368.1		n.214+14471A>G		intron	N/A
	ENSG00000294133	ENST00000721369.1		n.290+14471A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 655 AN: 6080 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0455

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.00658

Gnomad MID AF: 0.0588

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.152

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: AS_VQSR AF: 0.108 AC: 659 AN: 6080 Hom.: 2 Cov.: 0 AF XY: 0.100 AC XY: 278 AN XY: 2772

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

African (AFR) AF: 0.233 AC: 351 AN: 1504

American (AMR) AF: 0.0761 AC: 58 AN: 762

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 15 AN: 144

East Asian (EAS) AF: 0.0427 AC: 27 AN: 632

South Asian (SAS) AF: 0.0833 AC: 23 AN: 276

European-Finnish (FIN) AF: 0.00658 AC: 1 AN: 152

Middle Eastern (MID) AF: 0.0714 AC: 2 AN: 28

European-Non Finnish (NFE) AF: 0.0683 AC: 167 AN: 2446

Other (OTH) AF: 0.141 AC: 13 AN: 92

⚠️ 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: 0.254 Hom.: 90

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.4
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs228173;

hg19: chr1-148947423;