chr16-64330705-C-T

Variant names:

• chr16-64330705-C-T
• rs1541694
• ENST00000561657.1:n.381+12824G>A

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 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: ENSG00000261028 ENST00000561657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

ENSG00000261028 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261028	ENST00000561657.1	n.381+12824G>A		intron_variant	Intron 1 of 4	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;