rs1761325

chr10-44401541-G-A

Variant summary

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

The XR_001747298.2(LOC107984179):n.2921G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,852 control chromosomes in the GnomAD database, including 2,156 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 0.16 (2156 hom., cov: 33)
• Consequence: LOC107984179 XR_001747298.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.2921G>A		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24379 AN: 151734 Hom.: 2152 Cov.: 33

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.161 AC: 24382 AN: 151852 Hom.: 2156 Cov.: 33 AF XY: 0.159 AC XY: 11789 AN XY: 74192

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.159

Alfa AF: 0.196 Hom.: 2938

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1761325; hg19: chr10-44896989; COSMIC: COSV55953557;