rs2000292

Positions:

• chr6-77457228-G-A

Variant summary

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

The XM_047419660.1(LOC105377864):​c.-3743+15795G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,786 control chromosomes in the GnomAD database, including 7,534 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 0.31 (7534 hom., cov: 32)
• Consequence: LOC105377864 XM_047419660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377864	XM_047419660.1	c.-3743+15795G>A		intron_variant			XP_047275616.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46814 AN: 151668 Hom.: 7529 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.309 AC: 46838 AN: 151786 Hom.: 7534 Cov.: 32 AF XY: 0.309 AC XY: 22911 AN XY: 74176

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.309

Alfa AF: 0.280 Hom.: 3730

Bravo AF: 0.321

Asia WGS AF: 0.364 AC: 1265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2000292; hg19: chr6-78166945;