rs1867485

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000261161	ENST00000808928.1	n.854+69G>A		intron_variant	Intron 4 of 4
ENSG00000261161	ENST00000808929.1	n.721+226G>A		intron_variant	Intron 5 of 5
ENSG00000261161	ENST00000808930.1	n.113+16619G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.500 AC: 1 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: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.462 AC: 12 AN: 26

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.690 AC: 28626 AN: 41462

American (AMR) AF: 0.547 AC: 8361 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1750 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3693 AN: 5156

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5544 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30823 AN: 67988

Other (OTH) AF: 0.532 AC: 1123 AN: 2110

Alfa AF: 0.489 Hom.: 83952

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1867485; hg19: chr16-86681031;