7-128208521-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710955.1(ENSG00000292309):n.835+1446C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,174 control chromosomes in the GnomAD database, including 47,343 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 0.78 (47343 hom., cov: 33)
• Consequence: ENST00000710955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901744	XR_007060516.1	n.780+1446C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710955.1	n.835+1446C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118524 AN: 152058 Hom.: 47338 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.779 AC: 118560 AN: 152174 Hom.: 47343 Cov.: 33 AF XY: 0.780 AC XY: 58034 AN XY: 74396

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.805

Alfa AF: 0.780 Hom.: 2602

Bravo AF: 0.761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2060736; hg19: chr7-127848574;