rs7088285

Positions:

• chr10-44392481-G-A
• chr10-44392481-G-C
• chr10-44392481-G-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+2649G>A 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 0.202 in 151,324 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3456 hom., cov: 31)
• Consequence: LOC107984179 XR_001747298.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.67+2649G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30550 AN: 151208 Hom.: 3446 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.202 AC: 30581 AN: 151324 Hom.: 3456 Cov.: 31 AF XY: 0.204 AC XY: 15044 AN XY: 73900

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.237

Alfa AF: 0.139 Hom.: 389

Bravo AF: 0.198

Asia WGS AF: 0.361 AC: 1253 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	0.90
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7088285; hg19: chr10-44887929;