16-51166620-T-G

Position:

• chr16-51166620-T-G

Variant summary

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

The ENST00000643626.1(ENSG00000285367):​n.51+14445T>G 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 0.738 in 152,060 control chromosomes in the GnomAD database, including 42,797 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 0.74 (42797 hom., cov: 32)
• Consequence: ENST00000643626.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643626.1	n.51+14445T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112139 AN: 151942 Hom.: 42778 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.738 AC: 112203 AN: 152060 Hom.: 42797 Cov.: 32 AF XY: 0.741 AC XY: 55074 AN XY: 74336

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.748

Alfa AF: 0.804 Hom.: 23835

Bravo AF: 0.713

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4785239; hg19: chr16-51200531;