ENST00000758119.1:n.214+2072G>A

Variant names:

• chr4-31395996-G-A
• rs6448771
• ENST00000758119.1:n.214+2072G>A

Variant summary

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

The ENST00000758119.1(ENSG00000298819):​n.214+2072G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,046 control chromosomes in the GnomAD database, including 37,795 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 0.69 (37795 hom., cov: 32)
• Consequence: ENSG00000298819 ENST00000758119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 9 publications found

Genes affected

ENSG00000298819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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
ENSG00000298819	ENST00000758119.1	n.214+2072G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105244 AN: 151928 Hom.: 37743 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.693 AC: 105348 AN: 152046 Hom.: 37795 Cov.: 32 AF XY: 0.682 AC XY: 50677 AN XY: 74298

African (AFR) AF: 0.838 AC: 34751 AN: 41472

American (AMR) AF: 0.535 AC: 8170 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2698 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1519 AN: 5168

South Asian (SAS) AF: 0.564 AC: 2722 AN: 4822

European-Finnish (FIN) AF: 0.630 AC: 6636 AN: 10540

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46473 AN: 67990

Other (OTH) AF: 0.685 AC: 1450 AN: 2116

Alfa AF: 0.681 Hom.: 125575

Bravo AF: 0.692

Asia WGS AF: 0.461 AC: 1603 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.38
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6448771; hg19: chr4-31397618;