7-115446970-T-C

Variant names:

• chr7-115446970-T-C
• rs1534378
• ENST00000753091.1:n.367+22172T>C

Variant summary

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

The ENST00000753091.1(ENSG00000298119):​n.367+22172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,036 control chromosomes in the GnomAD database, including 51,283 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 0.82 (51283 hom., cov: 33)
• Consequence: ENSG00000298119 ENST00000753091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 2 publications found

Genes affected

ENSG00000298119 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 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
ENSG00000298119	ENST00000753091.1	n.367+22172T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124240 AN: 151918 Hom.: 51254 Cov.: 33

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.818 AC: 124322 AN: 152036 Hom.: 51283 Cov.: 33 AF XY: 0.810 AC XY: 60173 AN XY: 74290

African (AFR) AF: 0.743 AC: 30846 AN: 41488

American (AMR) AF: 0.778 AC: 11887 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2847 AN: 3466

East Asian (EAS) AF: 0.654 AC: 3386 AN: 5178

South Asian (SAS) AF: 0.817 AC: 3945 AN: 4826

European-Finnish (FIN) AF: 0.768 AC: 8110 AN: 10566

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.890 AC: 60476 AN: 67916

Other (OTH) AF: 0.841 AC: 1777 AN: 2112

Alfa AF: 0.827 Hom.: 8447

Bravo AF: 0.813

Asia WGS AF: 0.735 AC: 2554 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.73
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1534378; hg19: chr7-115087024;