4-28225806-G-T

Variant summary

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

The XR_001741640.2(LOC105374557):n.830+10658G>T 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 0.0591 in 152,182 control chromosomes in the GnomAD database, including 642 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 0.059 (642 hom., cov: 32)
• Consequence: LOC105374557 XR_001741640.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

LOC105374557 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374557	XR_001741640.2	n.830+10658G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0590 AC: 8976 AN: 152064 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0591 AC: 8991 AN: 152182 Hom.: 642 Cov.: 32 AF XY: 0.0589 AC XY: 4386 AN XY: 74412

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0799

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00597

Gnomad4 OTH AF: 0.0562

Alfa AF: 0.00229 Hom.: 4

Bravo AF: 0.0682

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	14
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: rs10517138; hg19: chr4-28227428;