ENST00000775795.1:n.139-38428T>C

Variant names:

• chr7-84604517-A-G
• rs2079069
• ENST00000775795.1:n.139-38428T>C

Variant summary

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

The ENST00000775795.1(ENSG00000301054):​n.139-38428T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0297 in 152,228 control chromosomes in the GnomAD database, including 161 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 0.030 (161 hom., cov: 32)
• Consequence: ENSG00000301054 ENST00000775795.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

Genes affected

ENSG00000301054 (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 (EAS) allele frequency at 95% confidence interval = 0.146 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
ENSG00000301054	ENST00000775795.1	n.139-38428T>C		intron_variant	Intron 2 of 2
ENSG00000301054	ENST00000775796.1	n.211+26366T>C		intron_variant	Intron 3 of 3
ENSG00000301054	ENST00000775797.1	n.72-38428T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0297 AC: 4519 AN: 152110 Hom.: 161 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00444

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0297 AC: 4520 AN: 152228 Hom.: 161 Cov.: 32 AF XY: 0.0302 AC XY: 2251 AN XY: 74418

African (AFR) AF: 0.0580 AC: 2410 AN: 41570

American (AMR) AF: 0.0471 AC: 719 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3472

East Asian (EAS) AF: 0.155 AC: 800 AN: 5160

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4822

European-Finnish (FIN) AF: 0.00989 AC: 105 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00444 AC: 302 AN: 67998

Other (OTH) AF: 0.0260 AC: 55 AN: 2112

Alfa AF: 0.0248 Hom.: 18

Bravo AF: 0.0352

Asia WGS AF: 0.0770 AC: 266 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	3.7
DANN	Benign	0.36
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2079069; hg19: chr7-84233833;