rs232657

Variant names:

• chr20-7113887-C-T
• rs232657
• ENST00000425900.1:n.82-32470C>T

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.82-32470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,138 control chromosomes in the GnomAD database, including 15,470 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 0.42 (15470 hom., cov: 32)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

Genes affected

ENSG00000232271 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232271	ENST00000425900.1	n.82-32470C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63138 AN: 152020 Hom.: 15425 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.416 AC: 63244 AN: 152138 Hom.: 15470 Cov.: 32 AF XY: 0.411 AC XY: 30563 AN XY: 74366

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.411

Alfa AF: 0.319 Hom.: 3992

Bravo AF: 0.443

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs232657; hg19: chr20-7094534;