chr16-59727788-A-G

Position:

• chr16-59727788-A-G

Variant summary

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

The ENST00000565921.4(ENSG00000293012):​n.200-17493T>C 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 0.0392 in 152,204 control chromosomes in the GnomAD database, including 456 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 0.039 (456 hom., cov: 32)
• Consequence: ENST00000565921.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000565921.4	n.200-17493T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0391 AC: 5953 AN: 152086 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00883

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0392 AC: 5962 AN: 152204 Hom.: 456 Cov.: 32 AF XY: 0.0410 AC XY: 3048 AN XY: 74426

Gnomad4 AFR AF: 0.0568

Gnomad4 AMR AF: 0.0500

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0250

Gnomad4 NFE AF: 0.00884

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0166 Hom.: 36

Bravo AF: 0.0444

Asia WGS AF: 0.151 AC: 522 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965916; hg19: chr16-59761692;