rs1867485

chr16-86647425-G-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, non coding transcript 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: ENST00000565822.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000565822.1	n.327+69G>A		intron_variant, non_coding_transcript_variant		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;