rs7085387

Positions:

• chr10-58444842-G-A
• chr10-58444842-G-C
• chr10-58444842-G-T

Variant summary

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

The XR_945981.3(LOC105378316):​n.360+9185G>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 0.637 in 151,834 control chromosomes in the GnomAD database, including 32,903 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 0.64 (32903 hom., cov: 30)
• Consequence: LOC105378316 XR_945981.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

Genes affected

LOC105378316 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378316	XR_945981.3	n.360+9185G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96726 AN: 151716 Hom.: 32891 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.637 AC: 96769 AN: 151834 Hom.: 32903 Cov.: 30 AF XY: 0.636 AC XY: 47223 AN XY: 74206

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.635

Alfa AF: 0.713 Hom.: 18008

Bravo AF: 0.634

Asia WGS AF: 0.566 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085387; hg19: chr10-60204602;