rs10485083

Positions:

• chr6-6784051-C-G

Variant summary

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

The ENST00000689004.1(ENSG00000226281):​n.329+16792G>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 0.0659 in 152,228 control chromosomes in the GnomAD database, including 793 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 0.066 (793 hom., cov: 32)
• Consequence: ENST00000689004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928004	XR_007059429.1	n.485+10099G>C		intron_variant, non_coding_transcript_variant
LOC101928004	XR_007059430.1	n.276+10099G>C		intron_variant, non_coding_transcript_variant
LOC101928004	XR_007059432.1	n.276+10099G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000689004.1	n.329+16792G>C		intron_variant, non_coding_transcript_variant
	ENST00000702519.1	n.504+10099G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0657 AC: 9997 AN: 152110 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.00707

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00531

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0659 AC: 10035 AN: 152228 Hom.: 793 Cov.: 32 AF XY: 0.0659 AC XY: 4903 AN XY: 74422

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0685

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.00707

Gnomad4 NFE AF: 0.00529

Gnomad4 OTH AF: 0.0510

Alfa AF: 0.0401 Hom.: 56

Bravo AF: 0.0757

Asia WGS AF: 0.104 AC: 361 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	1.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485083; hg19: chr6-6784284;