rs4935720

chr10-57762376-C-T

Variant summary

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

The XR_001747454.1(LOC105378314):n.86-60991G>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 0.791 in 151,824 control chromosomes in the GnomAD database, including 47,896 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 0.79 (47896 hom., cov: 30)
• Consequence: LOC105378314 XR_001747454.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

Genes affected

LOC105378314 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378314	XR_001747454.1	n.86-60991G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120039 AN: 151706 Hom.: 47884 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.791 AC: 120089 AN: 151824 Hom.: 47896 Cov.: 30 AF XY: 0.787 AC XY: 58319 AN XY: 74146

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.820

Alfa AF: 0.812 Hom.: 6273

Bravo AF: 0.799

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.82
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4935720; hg19: chr10-59522136;