rs10490308

chr2-75255249-A-C

Variant summary

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

The NR_168009.1(LOC105374811):n.373-21261A>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 0.102 in 152,210 control chromosomes in the GnomAD database, including 857 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 0.10 (857 hom., cov: 32)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374811	NR_168009.1	n.373-21261A>C		intron_variant, non_coding_transcript_variant
LOC107985900	XR_001739546.2	n.29565-17387T>G		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.367-21261A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15561 AN: 152092 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.0690

Gnomad EAS AF: 0.00808

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.102 AC: 15572 AN: 152210 Hom.: 857 Cov.: 32 AF XY: 0.0998 AC XY: 7429 AN XY: 74424

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.0690

Gnomad4 EAS AF: 0.00810

Gnomad4 SAS AF: 0.0652

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.120

Alfa AF: 0.116 Hom.: 1439

Bravo AF: 0.104

Asia WGS AF: 0.0410 AC: 141 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.9
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490308; hg19: chr2-75482375;