16-51454831-C-T

Variant names:

• chr16-51454831-C-T
• rs10521030
• ENST00000643262.1:n.399+40271G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000643262.1(ENSG00000260850):​n.399+40271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 152,280 control chromosomes in the GnomAD database, including 143 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 0.024 (143 hom., cov: 32)
• Consequence: ENSG00000260850 ENST00000643262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 1 publications found

Genes affected

ENSG00000260850 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643262.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260850	ENST00000643262.1		n.399+40271G>A		intron	N/A
	ENSG00000260850	ENST00000646267.1		n.389+40271G>A		intron	N/A
	ENSG00000260850	ENST00000685077.3		n.396+40271G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3620 AN: 152162 Hom.: 143 Cov.: 32

Gnomad AFR AF: 0.00391

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0238 AC: 3631 AN: 152280 Hom.: 143 Cov.: 32 AF XY: 0.0277 AC XY: 2060 AN XY: 74472

African (AFR) AF: 0.00390 AC: 162 AN: 41556

American (AMR) AF: 0.0916 AC: 1400 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.114 AC: 589 AN: 5184

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4824

European-Finnish (FIN) AF: 0.0368 AC: 391 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 874 AN: 68024

Other (OTH) AF: 0.0261 AC: 55 AN: 2108

Alfa AF: 0.0165 Hom.: 72

Bravo AF: 0.0261

Asia WGS AF: 0.0820 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.50
DANN	Benign	0.61
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs10521030; hg19: chr16-51488742;