rs1532926

Positions:

• 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 ENST00000670665.1(ENSG00000260289):​n.335-16692T>G 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 0.342 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: ENST00000670665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

Genes affected

(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/exons	MANE	Protein	UniProt
LOC105371070	XR_001752068.3	n.434-16692T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670665.1	n.335-16692T>G		intron_variant, non_coding_transcript_variant
	ENST00000567103.2	n.302-16692T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000654046.1	n.335-16692T>G		intron_variant, non_coding_transcript_variant

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;