rs41526846

chr10-120292445-C-T

Variant summary

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

The XR_001747606.1(LOC105378515):n.993+3978C>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 0.0265 in 152,202 control chromosomes in the GnomAD database, including 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 0.026 (193 hom., cov: 32)
• Consequence: LOC105378515 XR_001747606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685

Genes affected

LOC105378515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378515	XR_001747606.1	n.993+3978C>T		intron_variant, non_coding_transcript_variant
LOC105378515	XR_001747605.1	n.703-1648C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4022 AN: 152090 Hom.: 192 Cov.: 32

Gnomad AFR AF: 0.00522

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0265 AC: 4029 AN: 152202 Hom.: 193 Cov.: 32 AF XY: 0.0294 AC XY: 2187 AN XY: 74416

Gnomad4 AFR AF: 0.00520

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0175

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0219 Hom.: 10

Bravo AF: 0.0314

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.96
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: rs41526846; hg19: chr10-122051957;