rs11648686

Variant names:

• chr16-52359484-A-G
• rs11648686
• ENST00000701553.1:n.118-3097T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701553.1(ENSG00000289907):​n.118-3097T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,192 control chromosomes in the GnomAD database, including 1,734 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 0.15 (1734 hom., cov: 32)
• Consequence: ENSG00000289907 ENST00000701553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

ENSG00000289907 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984901	XR_001752184.1	n.204-3097T>C		intron_variant	Intron 1 of 5
LOC107984901	XR_001752185.2	n.118-3097T>C		intron_variant	Intron 1 of 5
LOC107984901	XR_001752186.1	n.204-3097T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289907	ENST00000701553.1	n.118-3097T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22075 AN: 152074 Hom.: 1732 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.145 AC: 22094 AN: 152192 Hom.: 1734 Cov.: 32 AF XY: 0.142 AC XY: 10547 AN XY: 74430

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.00366

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.150

Alfa AF: 0.169 Hom.: 3051

Bravo AF: 0.144

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11648686; hg19: chr16-52393396;