ENST00000400371.2:n.1985+6560C>T

Variant names:

• chr20-46449335-G-A
• rs460869
• ENST00000400371.2:n.1985+6560C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400371.2(ENSG00000293461):​n.1985+6560C>T variant causes a intron 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: ENSG00000293461 ENST00000400371.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 3 publications found

Genes affected

ENSG00000293461 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293461	ENST00000400371.2	n.1985+6560C>T		intron_variant	Intron 3 of 3	1
ENSG00000293461	ENST00000849666.1	n.357+8340C>T		intron_variant	Intron 2 of 2
ENSG00000293461	ENST00000849667.1	n.421+8262C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.658 AC: 27294 AN: 41456

American (AMR) AF: 0.322 AC: 4926 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1633 AN: 5174

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1969 AN: 10570

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20931 AN: 67952

Other (OTH) AF: 0.381 AC: 806 AN: 2116

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs460869; hg19: chr20-45077974;