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

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000753888.1(ENSG00000298207):​n.306+30087G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 151,998 control chromosomes in the GnomAD database, including 6 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 0.0063 (6 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=-0.87).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00634 (963/151998) while in subpopulation AFR AF = 0.0218 (903/41444). AF 95% confidence interval is 0.0206. There are 6 homozygotes in GnomAd4. There are 436 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374497	XR_001739421.3	n.216+30087G>C		intron_variant	Intron 2 of 3
LOC105374497	XR_001739422.1	n.1665+30087G>C		intron_variant	Intron 2 of 3
LOC105374497	XR_001739423.1	n.216+30087G>C		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>C		intron_variant	Intron 3 of 4
ENSG00000298207	ENST00000753889.1	n.306+30087G>C		intron_variant	Intron 3 of 5
ENSG00000298207	ENST00000753890.1	n.402+30087G>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.00629 AC: 956 AN: 151880 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00282

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00431

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

GnomAD4 genome AF: 0.00634 AC: 963 AN: 151998 Hom.: 6 Cov.: 31 AF XY: 0.00587 AC XY: 436 AN XY: 74278

African (AFR) AF: 0.0218 AC: 903 AN: 41444

American (AMR) AF: 0.00281 AC: 43 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5148

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 67960

Other (OTH) AF: 0.00426 AC: 9 AN: 2112

Alfa AF: 0.00 Hom.: 17967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.76
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;