rs989631

Variant names:

• chr4-23044899-G-A
• rs989631
• ENST00000511453.5:n.286-10940G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-23044899-G-A
• chr4-23044899-G-T

Variant summary

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

The ENST00000511453.5(ENSG00000248837):​n.286-10940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,880 control chromosomes in the GnomAD database, including 7,804 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 0.30 (7804 hom., cov: 32)
• Consequence: ENSG00000248837 ENST00000511453.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 0 publications found

Genes affected

ENSG00000248837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374524	XR_007058432.1	n.305-38798G>A		intron_variant	Intron 3 of 7
LOC105374524	XR_007058433.1	n.305-38798G>A		intron_variant	Intron 3 of 7
LOC105374524	XR_007058434.1	n.305-38798G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248837	ENST00000511453.5	n.286-10940G>A		intron_variant	Intron 3 of 3	3
ENSG00000248837	ENST00000652324.1	n.302-38798G>A		intron_variant	Intron 3 of 9
ENSG00000248837	ENST00000653008.1	n.431+4117G>A		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45074 AN: 151762 Hom.: 7794 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.297 AC: 45123 AN: 151880 Hom.: 7804 Cov.: 32 AF XY: 0.301 AC XY: 22328 AN XY: 74250

African (AFR) AF: 0.382 AC: 15821 AN: 41414

American (AMR) AF: 0.405 AC: 6171 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3594 AN: 5146

South Asian (SAS) AF: 0.273 AC: 1311 AN: 4804

European-Finnish (FIN) AF: 0.240 AC: 2532 AN: 10554

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14320 AN: 67934

Other (OTH) AF: 0.282 AC: 595 AN: 2108

Alfa AF: 0.148 Hom.: 277

Bravo AF: 0.320

Asia WGS AF: 0.484 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.38
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs989631; hg19: chr4-23046522;