rs10519979

Variant names:

• chr4-148713799-A-G
• rs10519979
• ENST00000661928.1:n.223-152958A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-148713799-A-G
• chr4-148713799-A-T

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-152958A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,912 control chromosomes in the GnomAD database, including 26,081 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 0.56 (26081 hom., cov: 31)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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.223-152958A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85185 AN: 151798 Hom.: 26050 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.561 AC: 85259 AN: 151912 Hom.: 26081 Cov.: 31 AF XY: 0.552 AC XY: 40999 AN XY: 74218

African (AFR) AF: 0.795 AC: 32936 AN: 41450

American (AMR) AF: 0.394 AC: 6017 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3472

East Asian (EAS) AF: 0.158 AC: 812 AN: 5128

South Asian (SAS) AF: 0.338 AC: 1628 AN: 4814

European-Finnish (FIN) AF: 0.494 AC: 5199 AN: 10520

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34724 AN: 67938

Other (OTH) AF: 0.583 AC: 1231 AN: 2110

Alfa AF: 0.547 Hom.: 2959

Bravo AF: 0.566

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.28
PhyloP100		-0.50

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: rs10519979;

hg19: chr4-149634951;