rs2428486

Positions:

• chr6-31386327-T-C

Variant summary

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

The XR_007059542.1(LOC124901300):​n.75-936T>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 0.419 in 152,064 control chromosomes in the GnomAD database, including 14,069 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 0.42 (14069 hom., cov: 32)
• Consequence: LOC124901300 XR_007059542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LOC124901300 (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 (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901300	XR_007059542.1	n.75-936T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63580 AN: 151946 Hom.: 14046 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.419 AC: 63658 AN: 152064 Hom.: 14069 Cov.: 32 AF XY: 0.420 AC XY: 31204 AN XY: 74334

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.478

Alfa AF: 0.353 Hom.: 10125

Bravo AF: 0.440

Asia WGS AF: 0.398 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2428486; hg19: chr6-31354104;