rs232648

Variant names:

• chr20-7087789-T-G
• rs232648
• ENST00000425900.1:n.81+18095T>G

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.81+18095T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 152,110 control chromosomes in the GnomAD database, including 1,405 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 0.078 (1405 hom., cov: 32)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

ENSG00000232271 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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.81+18095T>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11807 AN: 151992 Hom.: 1398 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00553

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0779 AC: 11852 AN: 152110 Hom.: 1405 Cov.: 32 AF XY: 0.0759 AC XY: 5648 AN XY: 74368

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.00553

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0465 Hom.: 101

Bravo AF: 0.0874

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
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: rs232648; hg19: chr20-7068436;