ENST00000753888.1:n.306+30087G>A

Variant names:

• chr2-40807085-C-T
• rs977867
• ENST00000753888.1:n.306+30087G>A

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.306+30087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,932 control chromosomes in the GnomAD database, including 19,310 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 0.48 (19310 hom., cov: 31)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 0 publications found

Genes affected

ENSG00000298207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374497	XR_001739421.3	n.216+30087G>A		intron_variant	Intron 2 of 3
LOC105374497	XR_001739422.1	n.1665+30087G>A		intron_variant	Intron 2 of 3
LOC105374497	XR_001739423.1	n.216+30087G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298207	ENST00000753888.1	n.306+30087G>A		intron_variant	Intron 3 of 4
ENSG00000298207	ENST00000753889.1	n.306+30087G>A		intron_variant	Intron 3 of 5
ENSG00000298207	ENST00000753890.1	n.402+30087G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72296 AN: 151814 Hom.: 19317 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.476 AC: 72307 AN: 151932 Hom.: 19310 Cov.: 31 AF XY: 0.479 AC XY: 35547 AN XY: 74240

African (AFR) AF: 0.241 AC: 10005 AN: 41432

American (AMR) AF: 0.403 AC: 6149 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1719 AN: 5148

South Asian (SAS) AF: 0.693 AC: 3339 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6369 AN: 10544

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40876 AN: 67940

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.550 Hom.: 17967

Bravo AF: 0.446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs977867; hg19: chr2-41034225;