rs10485620

Variant names:

• chr20-51948629-T-C
• rs10485620
• ENST00000732944.1:n.91-34815A>G

Variant summary

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

The ENST00000732944.1(ENSG00000295844):​n.91-34815A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,032 control chromosomes in the GnomAD database, including 3,033 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 0.19 (3033 hom., cov: 32)
• Consequence: ENSG00000295844 ENST00000732944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 8 publications found

Genes affected

ENSG00000295844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732944.1. 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
	ENSG00000295844	ENST00000732944.1		n.91-34815A>G		intron	N/A
	ENSG00000295844	ENST00000732945.1		n.90-48392A>G		intron	N/A
	ENSG00000295844	ENST00000732946.1		n.286+12739A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29196 AN: 151912 Hom.: 3021 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.192 AC: 29247 AN: 152032 Hom.: 3033 Cov.: 32 AF XY: 0.194 AC XY: 14397 AN XY: 74298

African (AFR) AF: 0.199 AC: 8244 AN: 41476

American (AMR) AF: 0.281 AC: 4294 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3466

East Asian (EAS) AF: 0.123 AC: 637 AN: 5180

South Asian (SAS) AF: 0.0914 AC: 440 AN: 4812

European-Finnish (FIN) AF: 0.219 AC: 2310 AN: 10558

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12272 AN: 67974

Other (OTH) AF: 0.182 AC: 384 AN: 2108

Alfa AF: 0.185 Hom.: 10743

Bravo AF: 0.202

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.24
PhyloP100		0.21

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: rs10485620;

hg19: chr20-50565168;