rs10498919

chr6-78238016-G-C

Variant summary

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

The XR_002956359.2(LOC105377865):n.135-34063C>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 0.0446 in 152,050 control chromosomes in the GnomAD database, including 750 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 0.045 (750 hom., cov: 32)
• Consequence: LOC105377865 XR_002956359.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

LOC105377865 (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 (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377865	XR_002956359.2	n.135-34063C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6759 AN: 151934 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.00853

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00624

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0446 AC: 6776 AN: 152050 Hom.: 750 Cov.: 32 AF XY: 0.0527 AC XY: 3918 AN XY: 74284

Gnomad4 AFR AF: 0.00850

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.00836

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.0551

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.00624

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0285 Hom.: 43

Bravo AF: 0.0557

Asia WGS AF: 0.157 AC: 543 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	1.0
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498919; hg19: chr6-78947733;