rs300032

Variant names:

• chr16-86647390-G-A
• rs300032
• ENST00000565822.1:n.327+34G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-86647390-G-A
• chr16-86647390-G-T

Variant summary

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

The ENST00000565822.1(ENSG00000261161):​n.327+34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,196 control chromosomes in the GnomAD database, including 41,950 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 0.73 (41921 hom., cov: 33)
  • Exomes 𝑓: 0.86 (29 hom.)
• Consequence: ENSG00000261161 ENST00000565822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.849 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
ENSG00000261161	ENST00000565822.1	n.327+34G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111268 AN: 152000 Hom.: 41908 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.752

GnomAD4 exome AF: 0.859 AC: 67 AN: 78 Hom.: 29 Cov.: 0 AF XY: 0.885 AC XY: 46 AN XY: 52

Gnomad4 AFR exome AF: 0.750

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.857

Gnomad4 NFE exome AF: 0.885

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.732 AC: 111313 AN: 152118 Hom.: 41921 Cov.: 33 AF XY: 0.724 AC XY: 53834 AN XY: 74360

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.750

Alfa AF: 0.781 Hom.: 5769

Bravo AF: 0.716

Asia WGS AF: 0.592 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs300032; hg19: chr16-86680996;