rs1946519

Variant names:

• chr11-112164784-A-C
• rs1946519
• ENST00000532699.1:n.315-5635A>C

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-5635A>C 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 152,002 control chromosomes in the GnomAD database, including 26,943 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 (26943 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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.315-5635A>C		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.320-5635A>C		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.315-5635A>C		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90160 AN: 151884 Hom.: 26905 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.536

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: 90251 AN: 152002 Hom.: 26943 Cov.: 32 AF XY: 0.591 AC XY: 43880 AN XY: 74274

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.583

Alfa AF: 0.591 Hom.: 16353

Bravo AF: 0.593

Asia WGS AF: 0.609 AC: 2117 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	6.7
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs1946519; hg19: chr11-112035507;