ENST00000775347.1:n.290+39313T>G

Variant names:

• chr7-12055340-A-C
• rs1035147
• ENST00000775347.1:n.290+39313T>G

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.290+39313T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,942 control chromosomes in the GnomAD database, including 1,304 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 0.12 (1304 hom., cov: 31)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 5 publications found

Genes affected

ENSG00000300984 (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 (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901589	XR_007060211.1	n.85+39313T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300984	ENST00000775347.1	n.290+39313T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18398 AN: 151824 Hom.: 1301 Cov.: 31

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.121 AC: 18417 AN: 151942 Hom.: 1304 Cov.: 31 AF XY: 0.119 AC XY: 8854 AN XY: 74282

African (AFR) AF: 0.0457 AC: 1893 AN: 41442

American (AMR) AF: 0.144 AC: 2190 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.108 AC: 554 AN: 5152

South Asian (SAS) AF: 0.125 AC: 600 AN: 4808

European-Finnish (FIN) AF: 0.106 AC: 1122 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10804 AN: 67930

Other (OTH) AF: 0.151 AC: 318 AN: 2106

Alfa AF: 0.151 Hom.: 6082

Bravo AF: 0.123

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.43
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1035147; hg19: chr7-12094966;