rs10519980

Variant names:

• chr4-148713873-C-T
• rs10519980
• ENST00000661928.1:n.223-152884C>T

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-152884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,934 control chromosomes in the GnomAD database, including 4,007 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 0.22 (4007 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 16 publications found

Genes affected

ENSG00000287292 (HGNC:58892):

LOC107986195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.223-152884C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32855 AN: 151818 Hom.: 4008 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.216 AC: 32873 AN: 151934 Hom.: 4007 Cov.: 32 AF XY: 0.210 AC XY: 15579 AN XY: 74236

African (AFR) AF: 0.330 AC: 13677 AN: 41426

American (AMR) AF: 0.158 AC: 2409 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3472

East Asian (EAS) AF: 0.0621 AC: 321 AN: 5166

South Asian (SAS) AF: 0.149 AC: 716 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1213 AN: 10522

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13266 AN: 67968

Other (OTH) AF: 0.216 AC: 452 AN: 2096

Alfa AF: 0.201 Hom.: 10643

Bravo AF: 0.228

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		-0.52

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: rs10519980;

hg19: chr4-149635025;