chr2-51483165-T-C

Position:

• chr2-51483165-T-C

Variant summary

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

The NR_135237.1(LOC730100):​n.695-44437T>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 0.338 in 151,986 control chromosomes in the GnomAD database, including 9,975 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 0.34 (9975 hom., cov: 32)
• Consequence: LOC730100 NR_135237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC730100	NR_135237.1	n.695-44437T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000440698.1	n.695-44437T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51308 AN: 151868 Hom.: 9927 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.338 AC: 51422 AN: 151986 Hom.: 9975 Cov.: 32 AF XY: 0.347 AC XY: 25750 AN XY: 74250

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.328

Alfa AF: 0.272 Hom.: 815

Bravo AF: 0.346

Asia WGS AF: 0.549 AC: 1903 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919417; hg19: chr2-51710303;