rs7020422

chr9-105114945-G-A

Variant summary

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

The ENST00000666856.1(ENSG00000286536):n.1857+52675C>T 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 0.267 in 152,172 control chromosomes in the GnomAD database, including 6,902 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 0.27 (6902 hom., cov: 33)
• Consequence: ENST00000666856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376197	XR_930205.3	n.177-3786G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666856.1	n.1857+52675C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40484 AN: 152054 Hom.: 6875 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.267 AC: 40557 AN: 152172 Hom.: 6902 Cov.: 33 AF XY: 0.263 AC XY: 19540 AN XY: 74422

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.242

Alfa AF: 0.222 Hom.: 809

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.6
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7020422; hg19: chr9-107877226;