16-77008383-G-C

Variant names:

• chr16-77008383-G-C
• rs10514406
• ENST00000805261.1:n.420-74C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000805261.1(ENSG00000304662):​n.420-74C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 151,922 control chromosomes in the GnomAD database, including 260 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 0.038 (260 hom., cov: 32)
• Consequence: ENSG00000304662 ENST00000805261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 0 publications found

Genes affected

ENSG00000304662 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805261.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304662	ENST00000805261.1		n.420-74C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5743 AN: 151806 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0291

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00478

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0379 AC: 5753 AN: 151922 Hom.: 260 Cov.: 32 AF XY: 0.0376 AC XY: 2789 AN XY: 74252

African (AFR) AF: 0.105 AC: 4359 AN: 41426

American (AMR) AF: 0.0181 AC: 277 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3470

East Asian (EAS) AF: 0.101 AC: 519 AN: 5144

South Asian (SAS) AF: 0.0291 AC: 140 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10510

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.00478 AC: 325 AN: 67982

Other (OTH) AF: 0.0351 AC: 74 AN: 2108

Alfa AF: 0.0235 Hom.: 16

Bravo AF: 0.0423

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.40
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10514406; hg19: chr16-77042280;