rs754617

Positions:

• chr10-44390894-C-G
• chr10-44390894-C-T

Variant summary

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

The XR_001747298.2(LOC107984179):​n.67+1062C>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 0.166 in 152,118 control chromosomes in the GnomAD database, including 2,745 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 0.17 (2745 hom., cov: 32)
• Consequence: LOC107984179 XR_001747298.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.67+1062C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25289 AN: 152000 Hom.: 2744 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.166 AC: 25289 AN: 152118 Hom.: 2745 Cov.: 32 AF XY: 0.170 AC XY: 12619 AN XY: 74360

Gnomad4 AFR AF: 0.0420

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.204

Alfa AF: 0.0632 Hom.: 87

Bravo AF: 0.171

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754617; hg19: chr10-44886342;