rs2157453

chr1-172894808-G-A

Variant summary

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

The ENST00000432694.2(ENSG00000224228):n.224-109474G>A 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 0.323 in 152,026 control chromosomes in the GnomAD database, including 9,355 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 0.32 (9355 hom., cov: 32)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 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.224-109474G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49153 AN: 151908 Hom.: 9351 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.323 AC: 49173 AN: 152026 Hom.: 9355 Cov.: 32 AF XY: 0.332 AC XY: 24673 AN XY: 74300

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.327

Alfa AF: 0.269 Hom.: 2863

Bravo AF: 0.347

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.9
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157453; hg19: chr1-172863948;