rs6591904

chr11-80731676-A-G

Variant summary

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

The XR_001748502.2(LOC105369409):n.130+3267A>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 0.477 in 151,936 control chromosomes in the GnomAD database, including 17,657 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 0.48 (17657 hom., cov: 32)
• Consequence: LOC105369409 XR_001748502.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

LOC105369409 (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 (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369409	XR_001748502.2	n.130+3267A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72433 AN: 151818 Hom.: 17633 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.477 AC: 72501 AN: 151936 Hom.: 17657 Cov.: 32 AF XY: 0.478 AC XY: 35449 AN XY: 74234

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.471

Alfa AF: 0.463 Hom.: 2094

Bravo AF: 0.479

Asia WGS AF: 0.335 AC: 1159 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.1
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6591904; hg19: chr11-80442719;