rs11684394

Positions:

• chr2-75216947-C-T

Variant summary

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

The NR_168009.1(LOC105374811):​n.373-59563C>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 0.232 in 151,836 control chromosomes in the GnomAD database, including 4,946 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 0.23 (4946 hom., cov: 30)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374811	NR_168009.1	n.373-59563C>T		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.367-59563C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35260 AN: 151716 Hom.: 4947 Cov.: 30

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.232 AC: 35259 AN: 151836 Hom.: 4946 Cov.: 30 AF XY: 0.231 AC XY: 17168 AN XY: 74186

Gnomad4 AFR AF: 0.0735

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.257

Alfa AF: 0.297 Hom.: 11071

Bravo AF: 0.237

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11684394; hg19: chr2-75444073;