rs1864148

Variant names:

• chr16-64875566-C-A
• rs1864148
• ENST00000722731.1:n.155+4247C>A

Variant summary

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

The ENST00000722731.1(ENSG00000294320):​n.155+4247C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,166 control chromosomes in the GnomAD database, including 58,847 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 0.88 (58847 hom., cov: 32)
• Consequence: ENSG00000294320 ENST00000722731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 2 publications found

Genes affected

ENSG00000294320 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000294320	ENST00000722731.1	n.155+4247C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133585 AN: 152048 Hom.: 58801 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.879 AC: 133689 AN: 152166 Hom.: 58847 Cov.: 32 AF XY: 0.879 AC XY: 65355 AN XY: 74390

African (AFR) AF: 0.878 AC: 36482 AN: 41528

American (AMR) AF: 0.878 AC: 13402 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3130 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5167 AN: 5176

South Asian (SAS) AF: 0.934 AC: 4504 AN: 4824

European-Finnish (FIN) AF: 0.816 AC: 8634 AN: 10578

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59430 AN: 68002

Other (OTH) AF: 0.892 AC: 1884 AN: 2112

Alfa AF: 0.883 Hom.: 98404

Bravo AF: 0.884

Asia WGS AF: 0.954 AC: 3320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.41
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs1864148; hg19: chr16-64909469;