rs1074651

Variant names:

• chr16-64338708-T-C
• rs1074651
• ENST00000561657.1:n.381+4821A>G

Variant summary

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

The ENST00000561657.1(ENSG00000261028):​n.381+4821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,008 control chromosomes in the GnomAD database, including 10,756 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 (10756 hom., cov: 32)
• Consequence: ENSG00000261028 ENST00000561657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

ENSG00000261028 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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+4821A>G		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56070 AN: 151888 Hom.: 10740 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.369 AC: 56128 AN: 152008 Hom.: 10756 Cov.: 32 AF XY: 0.369 AC XY: 27401 AN XY: 74288

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.339

Alfa AF: 0.333 Hom.: 3960

Bravo AF: 0.380

Asia WGS AF: 0.323 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074651; hg19: chr16-64372612;