2-75202762-A-G

Variant summary

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

The NR_168009.1(LOC105374811):n.372+46447A>G 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 0.151 in 152,184 control chromosomes in the GnomAD database, including 2,290 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 0.15 (2290 hom., cov: 33)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374811	NR_168009.1	n.372+46447A>G		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.366+46447A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22883 AN: 152066 Hom.: 2292 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.151 AC: 22907 AN: 152184 Hom.: 2290 Cov.: 33 AF XY: 0.153 AC XY: 11400 AN XY: 74422

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.145

Alfa AF: 0.115 Hom.: 302

Bravo AF: 0.158

Asia WGS AF: 0.250 AC: 865 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.5
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59099335; hg19: chr2-75429888;