rs35703946

Variant names:

• chr16-85987899-G-A
• rs35703946
• ENST00000644960.1:n.793+85C>T

Variant summary

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

The ENST00000644960.1(ENSG00000285012):​n.793+85C>T variant causes a intron 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: ENSG00000285012 ENST00000644960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 12 publications found

Genes affected

ENSG00000285012 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285012	ENST00000644960.1	n.793+85C>T		intron_variant	Intron 2 of 2
ENSG00000285012	ENST00000787897.1	n.284-842C>T		intron_variant	Intron 2 of 2
ENSG00000285012	ENST00000787898.1	n.693-842C>T		intron_variant	Intron 1 of 1
ENSG00000285012	ENST00000787899.1	n.127+85C>T		intron_variant	Intron 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.155 AC: 9 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.0925 AC: 3822 AN: 41326

American (AMR) AF: 0.0767 AC: 1171 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.0861 AC: 444 AN: 5156

South Asian (SAS) AF: 0.0596 AC: 284 AN: 4766

European-Finnish (FIN) AF: 0.186 AC: 1958 AN: 10546

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9442 AN: 67926

Other (OTH) AF: 0.108 AC: 227 AN: 2104

Alfa AF: 0.123 Hom.: 482

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs35703946; hg19: chr16-86021505;