rs1867485

Variant names:

• chr16-86647425-G-A
• rs1867485
• ENST00000565822.1:n.327+69G>A

Variant summary

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

The ENST00000565822.1(ENSG00000261161):​n.327+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,080 control chromosomes in the GnomAD database, including 23,720 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 0.55 (23716 hom., cov: 32)
  • Exomes 𝑓: 0.47 (4 hom.)
• Consequence: ENSG00000261161 ENST00000565822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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+69G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83346 AN: 151930 Hom.: 23664 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.525

GnomAD4 exome AF: 0.469 AC: 15 AN: 32 Hom.: 4 AF XY: 0.500 AC XY: 13 AN XY: 26

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.462

GnomAD4 genome AF: 0.549 AC: 83458 AN: 152048 Hom.: 23716 Cov.: 32 AF XY: 0.553 AC XY: 41079 AN XY: 74306

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.532

Alfa AF: 0.476 Hom.: 36984

Bravo AF: 0.558

Asia WGS AF: 0.660 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1867485; hg19: chr16-86681031;