4-94693127-C-T

Variant names:

• chr4-94693127-C-T
• rs17022027
• ENST00000514304.1:n.95-9323C>T

Variant summary

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

The ENST00000514304.1(ENSG00000249951):​n.95-9323C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 151,700 control chromosomes in the GnomAD database, including 957 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 0.098 (957 hom., cov: 31)
• Consequence: ENSG00000249951 ENST00000514304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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.95-9323C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14915 AN: 151582 Hom.: 954 Cov.: 31

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0985 AC: 14935 AN: 151700 Hom.: 957 Cov.: 31 AF XY: 0.100 AC XY: 7435 AN XY: 74134

African (AFR) AF: 0.0778 AC: 3216 AN: 41356

American (AMR) AF: 0.193 AC: 2933 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 299 AN: 3460

East Asian (EAS) AF: 0.320 AC: 1642 AN: 5128

South Asian (SAS) AF: 0.111 AC: 531 AN: 4794

European-Finnish (FIN) AF: 0.0545 AC: 573 AN: 10512

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0783 AC: 5321 AN: 67924

Other (OTH) AF: 0.112 AC: 237 AN: 2108

Alfa AF: 0.0852 Hom.: 1887

Bravo AF: 0.109

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.33
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: rs17022027; hg19: chr4-95614278;