2-75199777-G-C

Position:

• chr2-75199777-G-C

Variant summary

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

The NR_168009.1(LOC105374811):​n.372+43462G>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 0.0615 in 152,430 control chromosomes in the GnomAD database, including 333 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 0.062 (333 hom., cov: 33)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374811	NR_168009.1	n.372+43462G>C		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.366+43462G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9363 AN: 152184 Hom.: 334 Cov.: 33

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.00811

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0809

Gnomad OTH AF: 0.0616

GnomAD4 exome AF: 0.0625 AC: 8 AN: 128 Hom.: 0 AF XY: 0.0732 AC XY: 6 AN XY: 82

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0761

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.0615 AC: 9367 AN: 152302 Hom.: 333 Cov.: 33 AF XY: 0.0592 AC XY: 4408 AN XY: 74484

Gnomad4 AFR AF: 0.0530

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.00813

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0809

Gnomad4 OTH AF: 0.0619

Alfa AF: 0.0267 Hom.: 19

Bravo AF: 0.0609

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10210648; hg19: chr2-75426903;