chr16-75505538-C-T

Position:

• chr16-75505538-C-T

Variant summary

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

The variant allele was found at a frequency of 0.0511 in 151,964 control chromosomes in the GnomAD database, including 387 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 0.051 (387 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.75505538C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291051	ENST00000571737.1	n.79-163G>A		intron_variant		3
ENSG00000291051	ENST00000690952.1	n.49-255G>A		intron_variant
ENSG00000291051	ENST00000701489.1	n.77-160G>A		intron_variant
ENSG00000291051	ENST00000701583.1	n.190-160G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0510 AC: 7749 AN: 151856 Hom.: 385 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.0554

Gnomad FIN AF: 0.00531

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0161

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0511 AC: 7763 AN: 151964 Hom.: 387 Cov.: 31 AF XY: 0.0508 AC XY: 3777 AN XY: 74280

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0244

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.0550

Gnomad4 FIN AF: 0.00531

Gnomad4 NFE AF: 0.0161

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0230 Hom.: 147

Bravo AF: 0.0559

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2550893; hg19: chr16-75539436;