rs1946518

Variant names:

• chr11-112164735-T-G
• rs1946518
• ENST00000532699.1:n.315-5684T>G

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-5684T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,882 control chromosomes in the GnomAD database, including 26,910 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 0.59 (26910 hom., cov: 31)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935
• Publications: 533 publications found

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 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
ENSG00000255292	ENST00000532699.1	n.315-5684T>G		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.320-5684T>G		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.315-5684T>G		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90083 AN: 151764 Hom.: 26872 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.594 AC: 90174 AN: 151882 Hom.: 26910 Cov.: 31 AF XY: 0.591 AC XY: 43839 AN XY: 74216

African (AFR) AF: 0.640 AC: 26491 AN: 41406

American (AMR) AF: 0.536 AC: 8183 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2464 AN: 5152

South Asian (SAS) AF: 0.684 AC: 3301 AN: 4824

European-Finnish (FIN) AF: 0.537 AC: 5656 AN: 10534

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40434 AN: 67922

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.593 Hom.: 82425

Bravo AF: 0.593

Asia WGS AF: 0.608 AC: 2112 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1946518; hg19: chr11-112035458;