rs4888473

chr16-76128092-G-Achr16-76128092-G-C

Variant summary

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

The ENST00000564561.1(ENSG00000260223):n.262+12270C>T 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 0.22 in 152,014 control chromosomes in the GnomAD database, including 5,138 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 0.22 (5138 hom., cov: 32)
• Consequence: ENST00000564561.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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
	ENST00000564561.1	n.262+12270C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33350 AN: 151896 Hom.: 5120 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.220 AC: 33384 AN: 152014 Hom.: 5138 Cov.: 32 AF XY: 0.231 AC XY: 17185 AN XY: 74294

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.251

Alfa AF: 0.185 Hom.: 426

Bravo AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.3
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4888473; hg19: chr16-76161990;