20-46449335-G-A

Position:

• chr20-46449335-G-A

Variant summary

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

The ENST00000400371.2(ENSG00000293461):​n.1985+6560C>T 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 0.4 in 152,046 control chromosomes in the GnomAD database, including 14,233 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 0.40 (14233 hom., cov: 32)
• Consequence: ENST00000400371.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

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 = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000400371.2	n.1985+6560C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60673 AN: 151928 Hom.: 14183 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.400 AC: 60786 AN: 152046 Hom.: 14233 Cov.: 32 AF XY: 0.392 AC XY: 29143 AN XY: 74324

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.381

Alfa AF: 0.373 Hom.: 2092

Bravo AF: 0.422

Asia WGS AF: 0.372 AC: 1291 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	2.3
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: rs460869; hg19: chr20-45077974;