chr16-62947480-A-G

Variant names:

• chr16-62947480-A-G
• rs30864
• ENST00000734827.1:n.62-24700T>C

Variant summary

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

The ENST00000734827.1(ENSG00000260658):​n.62-24700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,464 control chromosomes in the GnomAD database, including 16,550 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 0.43 (16550 hom., cov: 29)
• Consequence: ENSG00000260658 ENST00000734827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 2 publications found

Genes affected

ENSG00000260658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734827.1. 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
	ENSG00000260658	ENST00000734827.1		n.62-24700T>C		intron	N/A
	ENSG00000260658	ENST00000734828.1		n.176-24700T>C		intron	N/A
	ENSG00000260658	ENST00000734829.1		n.57-24700T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65144 AN: 151348 Hom.: 16507 Cov.: 29

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.431 AC: 65231 AN: 151464 Hom.: 16550 Cov.: 29 AF XY: 0.428 AC XY: 31683 AN XY: 73970

African (AFR) AF: 0.720 AC: 29673 AN: 41240

American (AMR) AF: 0.322 AC: 4905 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1366 AN: 5118

South Asian (SAS) AF: 0.345 AC: 1649 AN: 4784

European-Finnish (FIN) AF: 0.333 AC: 3488 AN: 10484

Middle Eastern (MID) AF: 0.307 AC: 89 AN: 290

European-Non Finnish (NFE) AF: 0.325 AC: 22065 AN: 67854

Other (OTH) AF: 0.361 AC: 759 AN: 2100

Alfa AF: 0.387 Hom.: 1643

Bravo AF: 0.442

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs30864; hg19: chr16-62981384;