rs284924

Variant names:

• chr16-77009729-G-T
• rs284924
• ENST00000805261.1:n.420-1420C>A

Variant summary

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

The ENST00000805261.1(ENSG00000304662):​n.420-1420C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,092 control chromosomes in the GnomAD database, including 3,716 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 0.21 (3716 hom., cov: 33)
• Consequence: ENSG00000304662 ENST00000805261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304662	ENST00000805261.1		n.420-1420C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31920 AN: 151974 Hom.: 3714 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31914 AN: 152092 Hom.: 3716 Cov.: 33 AF XY: 0.206 AC XY: 15346 AN XY: 74348

African (AFR) AF: 0.120 AC: 4967 AN: 41504

American (AMR) AF: 0.219 AC: 3349 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3468

East Asian (EAS) AF: 0.173 AC: 891 AN: 5158

South Asian (SAS) AF: 0.141 AC: 680 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10568

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18425 AN: 67976

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.214 Hom.: 531

Bravo AF: 0.210

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.45
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs284924; hg19: chr16-77043626; COSMIC: COSV107150857;