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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511453.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248837	ENST00000511453.5	TSL:3	n.286-10940G>A		intron	N/A
	ENSG00000248837	ENST00000652324.1		n.302-38798G>A		intron	N/A
	ENSG00000248837	ENST00000653008.1		n.431+4117G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs989631;

hg19: chr4-23046522;