chr2-51821024-G-C

Position:

• chr2-51821024-G-C

Variant summary

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

The NR_135237.1(LOC730100):​n.840-40425G>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 0.528 in 151,950 control chromosomes in the GnomAD database, including 22,296 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 0.53 (22296 hom., cov: 31)
• Consequence: LOC730100 NR_135237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC730100	NR_135237.1	n.840-40425G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000440698.1	n.840-40425G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80071 AN: 151832 Hom.: 22260 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.528 AC: 80172 AN: 151950 Hom.: 22296 Cov.: 31 AF XY: 0.534 AC XY: 39658 AN XY: 74254

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.490

Alfa AF: 0.301 Hom.: 679

Bravo AF: 0.539

Asia WGS AF: 0.645 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017418; hg19: chr2-52048162;