rs10485512

Variant names:

• chr20-4425574-C-A
• rs10485512
• ENST00000661308.1:n.283-2511G>T

Variant summary

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

The ENST00000661308.1(ENSG00000236387):​n.283-2511G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,988 control chromosomes in the GnomAD database, including 10,569 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 0.35 (10569 hom., cov: 31)
• Consequence: ENSG00000236387 ENST00000661308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

ENSG00000236387 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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
ENSG00000236387	ENST00000661308.1	n.283-2511G>T		intron_variant	Intron 2 of 2
ENSG00000236387	ENST00000661705.1	n.379-2511G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52897 AN: 151870 Hom.: 10562 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.348 AC: 52925 AN: 151988 Hom.: 10569 Cov.: 31 AF XY: 0.354 AC XY: 26266 AN XY: 74252

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.372

Alfa AF: 0.409 Hom.: 18114

Bravo AF: 0.336

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485512; hg19: chr20-4406221;