rs9884781

Variant names:

• chr4-27988301-T-A
• rs9884781
• ENST00000846268.1:n.185-5138T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-27988301-T-A
• chr4-27988301-T-C
• chr4-27988301-T-G

Variant summary

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

The ENST00000846268.1(ENSG00000287389):​n.185-5138T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,850 control chromosomes in the GnomAD database, including 18,633 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 0.48 (18633 hom., cov: 31)
• Consequence: ENSG00000287389 ENST00000846268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 5 publications found

Genes affected

ENSG00000287389 (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 = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374552	XR_001741500.1	n.156-5188T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287389	ENST00000846268.1	n.185-5138T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72231 AN: 151732 Hom.: 18619 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.476 AC: 72276 AN: 151850 Hom.: 18633 Cov.: 31 AF XY: 0.487 AC XY: 36101 AN XY: 74198

African (AFR) AF: 0.288 AC: 11914 AN: 41426

American (AMR) AF: 0.610 AC: 9297 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3912 AN: 5132

South Asian (SAS) AF: 0.728 AC: 3506 AN: 4816

European-Finnish (FIN) AF: 0.497 AC: 5244 AN: 10552

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35360 AN: 67912

Other (OTH) AF: 0.494 AC: 1037 AN: 2100

Alfa AF: 0.488 Hom.: 2326

Bravo AF: 0.473

Asia WGS AF: 0.728 AC: 2533 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	2.7
DANN	Benign	0.21
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs9884781; hg19: chr4-27989923;