4-119396219-T-C

Variant names:

• chr4-119396219-T-C
• rs11098514
• ENST00000720595.1:n.691-6857T>C

Variant summary

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

The ENST00000720595.1(ENSG00000294020):​n.691-6857T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,028 control chromosomes in the GnomAD database, including 6,157 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 0.28 (6157 hom., cov: 32)
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 4 publications found

Genes affected

ENSG00000294020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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
ENSG00000294020	ENST00000720595.1	n.691-6857T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42919 AN: 151910 Hom.: 6154 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.283 AC: 42951 AN: 152028 Hom.: 6157 Cov.: 32 AF XY: 0.279 AC XY: 20764 AN XY: 74290

African (AFR) AF: 0.285 AC: 11802 AN: 41450

American (AMR) AF: 0.271 AC: 4132 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1974 AN: 5166

South Asian (SAS) AF: 0.176 AC: 847 AN: 4826

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10560

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19929 AN: 67972

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.272 Hom.: 918

Bravo AF: 0.291

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.91
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs11098514; hg19: chr4-120317374;