rs35703946

chr16-85987899-G-A

Variant summary

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

The ENST00000644960.1(ENSG00000285012):n.793+85C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,832 control chromosomes in the GnomAD database, including 1,129 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 0.12 (1128 hom., cov: 27)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: ENST00000644960.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644960.1	n.793+85C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17663 AN: 151642 Hom.: 1128 Cov.: 27

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.109

GnomAD4 exome AF: 0.125 AC: 9 AN: 72 Hom.: 1 AF XY: 0.103 AC XY: 6 AN XY: 58

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.116 AC: 17665 AN: 151760 Hom.: 1128 Cov.: 27 AF XY: 0.116 AC XY: 8624 AN XY: 74148

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.0596

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.108

Alfa AF: 0.129 Hom.: 329

Bravo AF: 0.107

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.9
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35703946; hg19: chr16-86021505;