rs1445065

chr3-106493651-A-G

Variant summary

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

The ENST00000668075.1(ENSG00000291293):n.210+7066T>C 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 0.265 in 152,050 control chromosomes in the GnomAD database, including 6,162 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 0.26 (6162 hom., cov: 32)
• Consequence: ENST00000668075.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929485	XR_007095992.1	n.1049+7066T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668075.1	n.210+7066T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40213 AN: 151932 Hom.: 6158 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.265 AC: 40247 AN: 152050 Hom.: 6162 Cov.: 32 AF XY: 0.268 AC XY: 19936 AN XY: 74366

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.282

Alfa AF: 0.216 Hom.: 5066

Bravo AF: 0.284

Asia WGS AF: 0.484 AC: 1681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.035
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1445065; hg19: chr3-106212498;