16-64330705-C-T

Position:

• chr16-64330705-C-T

Variant summary

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

The ENST00000561657.1(ENSG00000261028):​n.381+12824G>A 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 0.365 in 151,510 control chromosomes in the GnomAD database, including 10,460 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 0.37 (10460 hom., cov: 29)
• Consequence: ENST00000561657.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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
	ENST00000561657.1	n.381+12824G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55284 AN: 151392 Hom.: 10446 Cov.: 29

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.365 AC: 55335 AN: 151510 Hom.: 10460 Cov.: 29 AF XY: 0.365 AC XY: 27030 AN XY: 74052

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.336

Alfa AF: 0.331 Hom.: 4030

Bravo AF: 0.374

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541694; hg19: chr16-64364609;