rs1477156

chr2-75202015-T-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+45700T>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 0.575 in 152,020 control chromosomes in the GnomAD database, including 27,493 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 0.57 (27493 hom., cov: 32)
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374811	NR_168009.1	n.372+45700T>C		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.366+45700T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87260 AN: 151900 Hom.: 27454 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.575 AC: 87360 AN: 152020 Hom.: 27493 Cov.: 32 AF XY: 0.568 AC XY: 42180 AN XY: 74322

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.547

Alfa AF: 0.514 Hom.: 4270

Bravo AF: 0.595

Asia WGS AF: 0.452 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.93
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1477156; hg19: chr2-75429141;