rs2426496

Positions:

• chr20-54178708-T-G

Variant summary

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

The ENST00000655028.1(ENSG00000286587):​n.75+220T>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 0.652 in 151,950 control chromosomes in the GnomAD database, including 32,626 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 0.65 (32626 hom., cov: 32)
• Consequence: ENST00000655028.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.195+220T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655028.1	n.75+220T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99027 AN: 151832 Hom.: 32609 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.652 AC: 99086 AN: 151950 Hom.: 32626 Cov.: 32 AF XY: 0.652 AC XY: 48439 AN XY: 74258

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.632

Alfa AF: 0.661 Hom.: 4835

Bravo AF: 0.650

Asia WGS AF: 0.620 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2426496; hg19: chr20-52795247;