rs10498919

Variant names:

• chr6-78238016-G-C
• rs10498919
• ENST00000715178.1:n.1038-34063C>G

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.1038-34063C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,050 control chromosomes in the GnomAD database, including 750 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 0.045 (750 hom., cov: 32)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 4 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715178.1. 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
	ENSG00000230309	ENST00000715178.1		n.1038-34063C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6759 AN: 151934 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.00853

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00624

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0446 AC: 6776 AN: 152050 Hom.: 750 Cov.: 32 AF XY: 0.0527 AC XY: 3918 AN XY: 74284

African (AFR) AF: 0.00850 AC: 353 AN: 41522

American (AMR) AF: 0.183 AC: 2792 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5160

South Asian (SAS) AF: 0.0551 AC: 265 AN: 4808

European-Finnish (FIN) AF: 0.0999 AC: 1055 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00624 AC: 424 AN: 67966

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0285 Hom.: 43

Bravo AF: 0.0557

Asia WGS AF: 0.157 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		0.039

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: rs10498919;

hg19: chr6-78947733;