10-58484957-T-C

Position:

• chr10-58484957-T-C

Variant summary

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

The XR_945981.3(LOC105378316):​n.845+3473T>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 0.457 in 151,866 control chromosomes in the GnomAD database, including 16,111 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 0.46 (16111 hom., cov: 30)
• Consequence: LOC105378316 XR_945981.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

LOC105378316 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378316	XR_945981.3	n.845+3473T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69391 AN: 151748 Hom.: 16083 Cov.: 30

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.457 AC: 69464 AN: 151866 Hom.: 16111 Cov.: 30 AF XY: 0.464 AC XY: 34422 AN XY: 74236

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.454

Alfa AF: 0.430 Hom.: 5810

Bravo AF: 0.464

Asia WGS AF: 0.608 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7096154; hg19: chr10-60244717;