4-94692024-A-G

Variant names:

• chr4-94692024-A-G
• rs17339671
• ENST00000514304.1:n.95-10426A>G

Variant summary

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

The ENST00000514304.1(ENSG00000249951):​n.95-10426A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,230 control chromosomes in the GnomAD database, including 968 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 0.11 (968 hom., cov: 32)
• Consequence: ENSG00000249951 ENST00000514304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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.95-10426A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16854 AN: 152114 Hom.: 959 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.111 AC: 16882 AN: 152230 Hom.: 968 Cov.: 32 AF XY: 0.112 AC XY: 8299 AN XY: 74404

African (AFR) AF: 0.0944 AC: 3922 AN: 41530

American (AMR) AF: 0.0925 AC: 1415 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3468

East Asian (EAS) AF: 0.0734 AC: 380 AN: 5174

South Asian (SAS) AF: 0.0962 AC: 464 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1532 AN: 10610

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8222 AN: 68008

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.112 Hom.: 1100

Bravo AF: 0.107

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		0.65
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: rs17339671; hg19: chr4-95613175;