chr16-64924739-A-G

Variant names:

• chr16-64924739-A-G
• rs429065
• ENST00000722600.1:n.177+13858T>C

Variant summary

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

The ENST00000722600.1(ENSG00000294300):​n.177+13858T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,424 control chromosomes in the GnomAD database, including 3,871 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 (3871 hom., cov: 32)
• Consequence: ENSG00000294300 ENST00000722600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 7 publications found

Genes affected

ENSG00000294300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 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
ENSG00000294300	ENST00000722600.1	n.177+13858T>C		intron_variant	Intron 2 of 2
ENSG00000294300	ENST00000722601.1	n.72+15105T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32225 AN: 151332 Hom.: 3868 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.213 AC: 32242 AN: 151424 Hom.: 3871 Cov.: 32 AF XY: 0.209 AC XY: 15422 AN XY: 73954

African (AFR) AF: 0.100 AC: 4133 AN: 41272

American (AMR) AF: 0.209 AC: 3174 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1044 AN: 5142

South Asian (SAS) AF: 0.154 AC: 736 AN: 4786

European-Finnish (FIN) AF: 0.213 AC: 2211 AN: 10366

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.281 AC: 19079 AN: 67916

Other (OTH) AF: 0.227 AC: 477 AN: 2100

Alfa AF: 0.250 Hom.: 1984

Bravo AF: 0.209

Asia WGS AF: 0.143 AC: 497 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	0.34
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs429065; hg19: chr16-64958642;