4-119322567-T-C

Variant names:

• chr4-119322567-T-C
• rs2282688
• ENST00000720595.1:n.176-11761T>C

Variant summary

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

The ENST00000720595.1(ENSG00000294020):​n.176-11761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,928 control chromosomes in the GnomAD database, including 24,447 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 0.57 (24447 hom., cov: 32)
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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.176-11761T>C		intron_variant	Intron 1 of 5
ENSG00000294020	ENST00000720596.1	n.224-11761T>C		intron_variant	Intron 1 of 6
ENSG00000294020	ENST00000720597.1	n.238-11761T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86052 AN: 151810 Hom.: 24414 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.567 AC: 86151 AN: 151928 Hom.: 24447 Cov.: 32 AF XY: 0.564 AC XY: 41879 AN XY: 74244

African (AFR) AF: 0.559 AC: 23167 AN: 41420

American (AMR) AF: 0.605 AC: 9238 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2157 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3237 AN: 5150

South Asian (SAS) AF: 0.533 AC: 2573 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5392 AN: 10564

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38547 AN: 67924

Other (OTH) AF: 0.599 AC: 1261 AN: 2106

Alfa AF: 0.568 Hom.: 5916

Bravo AF: 0.579

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.71
PhyloP100		-0.26
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2282688; hg19: chr4-120243722;