10-57805368-A-T

Variant summary

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

The XR_001747454.1(LOC105378314):n.85+41924T>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 0.807 in 151,984 control chromosomes in the GnomAD database, including 50,038 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 0.81 (50038 hom., cov: 31)
• Consequence: LOC105378314 XR_001747454.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

Genes affected

LOC105378314 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378314	XR_001747454.1	n.85+41924T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122620 AN: 151866 Hom.: 50028 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.807 AC: 122669 AN: 151984 Hom.: 50038 Cov.: 31 AF XY: 0.803 AC XY: 59604 AN XY: 74268

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.828

Alfa AF: 0.833 Hom.: 6589

Bravo AF: 0.812

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.5
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1505918; hg19: chr10-59565128;