chr1-143405602-T-C

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985200	XR_001738207.2	n.257+14471A>G		intron_variant	Intron 2 of 2
LOC107985200	XR_001738208.2	n.287-3822A>G		intron_variant	Intron 2 of 2
LOC107985200	XR_007066535.1	n.259-11916A>G		intron_variant	Intron 2 of 2
LOC107985200	XR_007066536.1	n.263+14471A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294133	ENST00000721367.1	n.286+14471A>G		intron_variant	Intron 2 of 2
ENSG00000294133	ENST00000721368.1	n.214+14471A>G		intron_variant	Intron 2 of 2
ENSG00000294133	ENST00000721369.1	n.290+14471A>G		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs228173; hg19: chr1-148947423;