7-10110349-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001745088.2(LOC105375149):n.101-10125G>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 0.277 in 151,936 control chromosomes in the GnomAD database, including 10,193 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 0.28 (10193 hom., cov: 32)
• Consequence: LOC105375149 XR_001745088.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11

Genes affected

LOC105375149 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375149	XR_001745088.2	n.101-10125G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42056 AN: 151820 Hom.: 10147 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.277 AC: 42161 AN: 151936 Hom.: 10193 Cov.: 32 AF XY: 0.280 AC XY: 20781 AN XY: 74240

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.227

Alfa AF: 0.0675 Hom.: 105

Bravo AF: 0.288

Asia WGS AF: 0.308 AC: 1075 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	18
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7778619; hg19: chr7-10149976;