rs232648

Positions:

• chr20-7087789-T-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, non coding transcript 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: ENST00000425900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000425900.1	n.81+18095T>G		intron_variant, non_coding_transcript_variant		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;