rs232658

Positions:

• chr20-7113723-G-A
• chr20-7113723-G-C

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.82-32634G>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 0.41 in 151,806 control chromosomes in the GnomAD database, including 14,908 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 0.41 (14908 hom., cov: 31)
• Consequence: ENST00000425900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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.82-32634G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62163 AN: 151686 Hom.: 14869 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.410 AC: 62265 AN: 151806 Hom.: 14908 Cov.: 31 AF XY: 0.407 AC XY: 30159 AN XY: 74184

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.404

Alfa AF: 0.216 Hom.: 546

Bravo AF: 0.436

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs232658; hg19: chr20-7094370;