chr20-46448270-A-G

Position:

• chr20-46448270-A-G

Variant summary

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

The ENST00000400371.2(ENSG00000293461):​n.1985+7625T>C 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 152,012 control chromosomes in the GnomAD database, including 14,251 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 (14251 hom., cov: 32)
• Consequence: ENST00000400371.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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+7625T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60677 AN: 151894 Hom.: 14201 Cov.: 32

Gnomad AFR AF: 0.659

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: 60790 AN: 152012 Hom.: 14251 Cov.: 32 AF XY: 0.392 AC XY: 29158 AN XY: 74324

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.323

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: 0.357 Hom.: 1431

Bravo AF: 0.423

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs446112; hg19: chr20-45076909;