4-94670825-C-G

Variant names:

• chr4-94670825-C-G
• rs998071
• ENST00000719651.1:n.44+192C>G

Variant summary

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

The ENST00000719651.1(ENSG00000293888):​n.44+192C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,968 control chromosomes in the GnomAD database, including 7,361 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 (7361 hom., cov: 32)
• Consequence: ENSG00000293888 ENST00000719651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 13 publications found

Genes affected

ENSG00000293888 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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
ENSG00000293888	ENST00000719651.1	n.44+192C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46175 AN: 151850 Hom.: 7349 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.304 AC: 46197 AN: 151968 Hom.: 7361 Cov.: 32 AF XY: 0.303 AC XY: 22528 AN XY: 74242

African (AFR) AF: 0.218 AC: 9054 AN: 41466

American (AMR) AF: 0.293 AC: 4481 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1734 AN: 5156

South Asian (SAS) AF: 0.217 AC: 1043 AN: 4808

European-Finnish (FIN) AF: 0.333 AC: 3513 AN: 10534

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24269 AN: 67948

Other (OTH) AF: 0.325 AC: 687 AN: 2116

Alfa AF: 0.195 Hom.: 460

Bravo AF: 0.297

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.64
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs998071; hg19: chr4-95591976;