chr16-85947995-T-C

Variant names:

• chr16-85947995-T-C
• rs305088
• ENST00000645383.1:n.739T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645383.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285163	ENST00000645383.1		n.739T>C		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000285163	ENST00000646214.1		n.423T>C		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000285163	ENST00000646986.2		n.1061T>C		non_coding_transcript_exon	Exon 3 of 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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 10 AN: 12

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.896 AC: 37199 AN: 41538

American (AMR) AF: 0.731 AC: 11182 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4676 AN: 5186

South Asian (SAS) AF: 0.783 AC: 3759 AN: 4802

European-Finnish (FIN) AF: 0.781 AC: 8281 AN: 10600

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45343 AN: 67986

Other (OTH) AF: 0.690 AC: 1459 AN: 2116

Alfa AF: 0.707 Hom.: 52053

Bravo AF: 0.756

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.97
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs305088; hg19: chr16-85981601;