rs3865177

Positions:

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

Variant summary

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

The ENST00000650164.1(ENSG00000261285):​n.585-25403C>T 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 0.309 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: ENST00000650164.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650164.1	n.585-25403C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.336

Alfa AF: 0.352 Hom.: 15085

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3865177; hg19: chr16-82569552;