rs10485660

Variant names:

• chr20-39763637-A-G
• rs10485660
• ENST00000668185.1:n.280-318A>G

Variant summary

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

The ENST00000668185.1(ENSG00000229976):​n.280-318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 152,104 control chromosomes in the GnomAD database, including 1,233 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 0.087 (1233 hom., cov: 32)
• Consequence: ENSG00000229976 ENST00000668185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 1 publications found

Genes affected

ENSG00000229976 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668185.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229976	ENST00000668185.1		n.280-318A>G		intron	N/A
	ENSG00000297754	ENST00000750795.1		n.402-4483T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13218 AN: 151988 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00834

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0872 AC: 13268 AN: 152104 Hom.: 1233 Cov.: 32 AF XY: 0.0906 AC XY: 6736 AN XY: 74352

African (AFR) AF: 0.199 AC: 8235 AN: 41456

American (AMR) AF: 0.144 AC: 2193 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1394 AN: 5140

South Asian (SAS) AF: 0.0940 AC: 453 AN: 4818

European-Finnish (FIN) AF: 0.0219 AC: 232 AN: 10616

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00835 AC: 568 AN: 68014

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0555 Hom.: 79

Bravo AF: 0.104

Asia WGS AF: 0.195 AC: 677 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10485660;

hg19: chr20-38392279;