rs10660430

Positions:

• chr16-85933558-C-CATG

Variant summary

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

The ENST00000646214.1(ENSG00000285163):​n.77+8499_77+8501dup variant causes a intron, non coding transcript 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: ENST00000646214.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646214.1	n.77+8499_77+8501dup		intron_variant, non_coding_transcript_variant
	ENST00000645383.1	n.393+1285_393+1287dup		intron_variant, non_coding_transcript_variant

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;