rs1532926

Variant names:

• chr16-8023916-A-C
• rs1532926
• ENST00000567103.2:n.302-16692T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-8023916-A-C
• chr16-8023916-A-T

Variant summary

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

The ENST00000567103.2(ENSG00000260289):​n.302-16692T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,010 control chromosomes in the GnomAD database, including 9,294 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 0.34 (9294 hom., cov: 33)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 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
ENSG00000260289	ENST00000567103.2	n.302-16692T>G		intron_variant	Intron 1 of 3	5
ENSG00000260289	ENST00000654046.1	n.335-16692T>G		intron_variant	Intron 1 of 3
ENSG00000260289	ENST00000670665.1	n.335-16692T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51968 AN: 151892 Hom.: 9288 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.342 AC: 52014 AN: 152010 Hom.: 9294 Cov.: 33 AF XY: 0.337 AC XY: 25012 AN XY: 74304

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.370

Alfa AF: 0.348 Hom.: 4620

Bravo AF: 0.348

Asia WGS AF: 0.180 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1532926; hg19: chr16-8073918;