rs10518498

Variant names:

• chr4-126575722-A-G
• rs10518498
• ENST00000661809.1:n.149-110580T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661809.1(ENSG00000286251):​n.149-110580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 152,096 control chromosomes in the GnomAD database, including 202 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 0.040 (202 hom., cov: 32)
• Consequence: ENSG00000286251 ENST00000661809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

ENSG00000286251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286251	ENST00000661809.1	n.149-110580T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6046 AN: 151978 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.00959

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0397 AC: 6045 AN: 152096 Hom.: 202 Cov.: 32 AF XY: 0.0394 AC XY: 2927 AN XY: 74342

Gnomad4 AFR AF: 0.00958

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0635

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0517 Hom.: 136

Bravo AF: 0.0335

Asia WGS AF: 0.00810 AC: 28 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518498; hg19: chr4-127496877;