16-75505538-C-T

Variant names:

• chr16-75505538-C-T
• rs2550893
• ENST00000571737.1:n.79-163G>A

Variant summary

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

The ENST00000571737.1(ENSG00000291051):​n.79-163G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000291051 ENST00000571737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

Genes affected

ENSG00000291051 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291051	ENST00000571737.1	n.79-163G>A		intron_variant	Intron 1 of 2	3
ENSG00000291051	ENST00000690952.1	n.49-255G>A		intron_variant	Intron 1 of 3
ENSG00000291051	ENST00000701489.1	n.77-160G>A		intron_variant	Intron 1 of 2
ENSG00000291051	ENST00000701583.1	n.190-160G>A		intron_variant	Intron 2 of 3

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;