rs3865177

Variant names:

• chr16-82535947-G-A
• rs3865177
• ENST00000650164.1:n.585-25403C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-82535947-G-A
• chr16-82535947-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650164.1(ENSG00000261285):​n.585-25403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,050 control chromosomes in the GnomAD database, including 7,817 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 0.31 (7817 hom., cov: 33)
• Consequence: ENSG00000261285 ENST00000650164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 6 publications found

Genes affected

ENSG00000261285 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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
ENSG00000261285	ENST00000650164.1	n.585-25403C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46945 AN: 151930 Hom.: 7812 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.336

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 46963 AN: 152050 Hom.: 7817 Cov.: 33 AF XY: 0.308 AC XY: 22905 AN XY: 74308

African (AFR) AF: 0.194 AC: 8047 AN: 41484

American (AMR) AF: 0.299 AC: 4566 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1255 AN: 5188

South Asian (SAS) AF: 0.421 AC: 2028 AN: 4816

European-Finnish (FIN) AF: 0.337 AC: 3547 AN: 10540

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24890 AN: 67984

Other (OTH) AF: 0.336 AC: 710 AN: 2110

Alfa AF: 0.345 Hom.: 33096

Bravo AF: 0.300

Asia WGS AF: 0.321 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.42
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs3865177; hg19: chr16-82569552;