rs9320695

chr6-119563679-G-A

Variant summary

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

The NR_134600.1(LOC105377975):n.252+13284G>A 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 0.612 in 152,054 control chromosomes in the GnomAD database, including 29,673 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 0.61 (29673 hom., cov: 32)
• Consequence: LOC105377975 NR_134600.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.59

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377975	NR_134600.1	n.252+13284G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701940.1	n.324+13284G>A		intron_variant, non_coding_transcript_variant
	ENST00000692359.2	n.341+13284G>A		intron_variant, non_coding_transcript_variant
	ENST00000701050.1	n.314+13284G>A		intron_variant, non_coding_transcript_variant
	ENST00000701673.1	n.313+13280G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93037 AN: 151936 Hom.: 29648 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.612 AC: 93103 AN: 152054 Hom.: 29673 Cov.: 32 AF XY: 0.614 AC XY: 45679 AN XY: 74336

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.629

Alfa AF: 0.642 Hom.: 5530

Bravo AF: 0.602

Asia WGS AF: 0.616 AC: 2142 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.070
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9320695; hg19: chr6-119884844;