rs4699587

Variant names:

• chr4-94694618-A-G
• rs4699587
• ENST00000514304.1:n.95-7832A>G

Variant summary

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

The ENST00000514304.1(ENSG00000249951):​n.95-7832A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,232 control chromosomes in the GnomAD database, including 159 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 0.041 (159 hom., cov: 32)
• Consequence: ENSG00000249951 ENST00000514304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 7 publications found

Genes affected

ENSG00000249951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0586 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
ENSG00000249951	ENST00000514304.1	n.95-7832A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0408 AC: 6202 AN: 152114 Hom.: 159 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0407 AC: 6203 AN: 152232 Hom.: 159 Cov.: 32 AF XY: 0.0401 AC XY: 2981 AN XY: 74426

African (AFR) AF: 0.0108 AC: 450 AN: 41570

American (AMR) AF: 0.0347 AC: 531 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.00932 AC: 45 AN: 4826

European-Finnish (FIN) AF: 0.0699 AC: 741 AN: 10600

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4088 AN: 68000

Other (OTH) AF: 0.0497 AC: 105 AN: 2112

Alfa AF: 0.0487 Hom.: 247

Bravo AF: 0.0373

Asia WGS AF: 0.00751 AC: 26 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	0.37
DANN	Benign	0.61
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4699587; hg19: chr4-95615769;