rs10518111

chr4-72983374-G-A

Variant summary

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

The XR_938873.2(LOC105377273):n.281-13695G>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 0.0667 in 152,212 control chromosomes in the GnomAD database, including 701 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 0.067 (701 hom., cov: 32)
• Consequence: LOC105377273 XR_938873.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

LOC107986286 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986286	XR_001741718.1	n.318+1686C>T		intron_variant, non_coding_transcript_variant
LOC105377273	XR_938873.2	n.281-13695G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10099 AN: 152094 Hom.: 696 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0667 AC: 10148 AN: 152212 Hom.: 701 Cov.: 32 AF XY: 0.0662 AC XY: 4926 AN XY: 74436

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.0189

Gnomad4 FIN AF: 0.00988

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0366 Hom.: 241

Bravo AF: 0.0802

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.6
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518111; hg19: chr4-73849091;