chr16-49334277-A-G

Variant names:

• chr16-49334277-A-G
• rs36507
• ENST00000564048.2:n.326-2384A>G

Variant summary

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

The ENST00000564048.2(ENSG00000279249):​n.326-2384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 151,864 control chromosomes in the GnomAD database, including 37,958 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 0.69 (37958 hom., cov: 29)
• Consequence: ENSG00000279249 ENST00000564048.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 9 publications found

Genes affected

ENSG00000279249 (HGNC:56730):

LOC124903689 (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 (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903689	XR_007065068.1	n.6509-2384A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279249	ENST00000564048.2	n.326-2384A>G		intron_variant	Intron 2 of 3	6
ENSG00000279249	ENST00000623424.2	n.386+3621A>G		intron_variant	Intron 2 of 4	6
ENSG00000279249	ENST00000643467.1	n.848+3621A>G		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104820 AN: 151746 Hom.: 37903 Cov.: 29

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.691 AC: 104932 AN: 151864 Hom.: 37958 Cov.: 29 AF XY: 0.694 AC XY: 51525 AN XY: 74218

African (AFR) AF: 0.857 AC: 35491 AN: 41430

American (AMR) AF: 0.759 AC: 11592 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2324 AN: 3466

East Asian (EAS) AF: 0.983 AC: 5072 AN: 5158

South Asian (SAS) AF: 0.799 AC: 3843 AN: 4808

European-Finnish (FIN) AF: 0.499 AC: 5242 AN: 10514

Middle Eastern (MID) AF: 0.703 AC: 204 AN: 290

European-Non Finnish (NFE) AF: 0.575 AC: 39034 AN: 67912

Other (OTH) AF: 0.718 AC: 1515 AN: 2110

Alfa AF: 0.640 Hom.: 12553

Bravo AF: 0.723

Asia WGS AF: 0.876 AC: 3045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs36507; hg19: chr16-49368188;