16-85947995-T-C

Position:

• chr16-85947995-T-C

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.739T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,220 control chromosomes in the GnomAD database, including 44,264 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 0.75 (44256 hom., cov: 33)
  • Exomes 𝑓: 0.77 (8 hom.)
• Consequence: ENSG00000285163 ENST00000645383.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371388	XR_001752395.1	n.383T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285163	ENST00000645383.1	n.739T>C		non_coding_transcript_exon_variant	3/4
ENSG00000285163	ENST00000646214.1	n.423T>C		non_coding_transcript_exon_variant	3/4
ENSG00000285163	ENST00000646986.1	n.1061T>C		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114625 AN: 152080 Hom.: 44190 Cov.: 33

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.686

GnomAD4 exome AF: 0.773 AC: 17 AN: 22 Hom.: 8 Cov.: 0 AF XY: 0.750 AC XY: 15 AN XY: 20

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.754 AC: 114756 AN: 152198 Hom.: 44256 Cov.: 33 AF XY: 0.760 AC XY: 56518 AN XY: 74400

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.690

Alfa AF: 0.714 Hom.: 7926

Bravo AF: 0.756

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.97
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305088; hg19: chr16-85981601;