rs2227203

chr1-172909883-T-Cchr1-172909883-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000432694.2(ENSG00000224228):n.224-94399T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,040 control chromosomes in the GnomAD database, including 39,029 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 0.70 (39029 hom., cov: 31)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432694.2	n.224-94399T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106129 AN: 151922 Hom.: 38975 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.699 AC: 106241 AN: 152040 Hom.: 39029 Cov.: 31 AF XY: 0.704 AC XY: 52347 AN XY: 74312

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.689

Alfa AF: 0.602 Hom.: 38414

Bravo AF: 0.723

Asia WGS AF: 0.794 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227203; hg19: chr1-172879023;