rs1504279

Positions:

• chr6-90830528-A-G

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-77528A>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 0.329 in 151,898 control chromosomes in the GnomAD database, including 8,414 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 0.33 (8414 hom., cov: 31)
• Consequence: LOC107986623 XR_001744259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986623	XR_001744259.1	n.1244-77528A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49915 AN: 151780 Hom.: 8408 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.329 AC: 49937 AN: 151898 Hom.: 8414 Cov.: 31 AF XY: 0.329 AC XY: 24449 AN XY: 74224

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.315

Alfa AF: 0.317 Hom.: 2936

Bravo AF: 0.322

Asia WGS AF: 0.341 AC: 1186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504279; hg19: chr6-91540246;