rs1986778

Variant names:

• chr11-87509702-G-A
• rs1986778
• ENST00000784851.1:n.476-43597G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-87509702-G-A
• chr11-87509702-G-C

Variant summary

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

The ENST00000784851.1(ENSG00000302190):​n.476-43597G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,878 control chromosomes in the GnomAD database, including 14,826 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 0.43 (14826 hom., cov: 31)
• Consequence: ENSG00000302190 ENST00000784851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 9 publications found

Genes affected

ENSG00000302190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984361	XR_001748316.2	n.319-43597G>A		intron_variant	Intron 2 of 3
LOC107984361	XR_002957260.2	n.396-43597G>A		intron_variant	Intron 3 of 7
LOC107984361	XR_002957261.2	n.319-43597G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302190	ENST00000784851.1	n.476-43597G>A		intron_variant	Intron 2 of 2
ENSG00000302190	ENST00000784852.1	n.180-43597G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65649 AN: 151760 Hom.: 14821 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.432 AC: 65663 AN: 151878 Hom.: 14826 Cov.: 31 AF XY: 0.430 AC XY: 31943 AN XY: 74210

African (AFR) AF: 0.320 AC: 13253 AN: 41416

American (AMR) AF: 0.426 AC: 6498 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2008 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1777 AN: 5138

South Asian (SAS) AF: 0.273 AC: 1317 AN: 4818

European-Finnish (FIN) AF: 0.521 AC: 5495 AN: 10540

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33733 AN: 67924

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.474 Hom.: 29973

Bravo AF: 0.426

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.014
DANN	Benign	0.18
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1986778; hg19: chr11-87220744;