rs2185710

Positions:

• chr6-113055846-A-G

Variant summary

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

The ENST00000670062.1(ENSG00000288560):​n.479+5333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,830 control chromosomes in the GnomAD database, including 21,353 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 0.51 (21353 hom., cov: 30)
• Consequence: ENSG00000288560 ENST00000670062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

Genes affected

ENSG00000288560 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986636	XR_001744308.2	n.226+5333A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288560	ENST00000670062.1	n.479+5333A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77889 AN: 151712 Hom.: 21352 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.513 AC: 77916 AN: 151830 Hom.: 21353 Cov.: 30 AF XY: 0.514 AC XY: 38158 AN XY: 74210

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.516

Alfa AF: 0.545 Hom.: 3096

Bravo AF: 0.498

Asia WGS AF: 0.527 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2185710; hg19: chr6-113377048;