rs2193405

Positions:

• chr2-75199842-T-A

Variant summary

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

The NR_168009.1(LOC105374811):​n.372+43527T>A 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 0.182 in 152,568 control chromosomes in the GnomAD database, including 3,105 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 0.18 (3096 hom., cov: 32)
  • Exomes 𝑓: 0.20 (9 hom.)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374811	NR_168009.1	n.372+43527T>A		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.366+43527T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27755 AN: 152026 Hom.: 3100 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.198 AC: 84 AN: 424 Hom.: 9 AF XY: 0.198 AC XY: 67 AN XY: 338

Gnomad4 AFR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.211

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.182 AC: 27752 AN: 152144 Hom.: 3096 Cov.: 32 AF XY: 0.181 AC XY: 13435 AN XY: 74356

Gnomad4 AFR AF: 0.0611

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0749

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.209

Alfa AF: 0.206 Hom.: 470

Bravo AF: 0.182

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193405; hg19: chr2-75426968;