rs10660430

Variant names:

• chr16-85933558-C-CATG
• rs10660430
• ENST00000645383.1:n.393+1284_393+1285insATG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000645383.1(ENSG00000285163):​n.393+1284_393+1285insATG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (14514 hom., cov: 0)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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
ENSG00000285163	ENST00000645383.1	n.393+1284_393+1285insATG		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.77+8498_77+8499insATG		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.456 AC: 62980 AN: 138088 Hom.: 14485 Cov.: 0

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.470

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.456 AC: 63050 AN: 138162 Hom.: 14514 Cov.: 0 AF XY: 0.460 AC XY: 30440 AN XY: 66184

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.434

Alfa AF: 0.388 Hom.: 1096

Asia WGS AF: 0.441 AC: 1528 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10660430; hg19: chr16-85967164;