rs1516174

Positions:

• chr2-51644203-A-G

Variant summary

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

The NR_135237.1(LOC730100):​n.753+116543A>G 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 0.775 in 151,394 control chromosomes in the GnomAD database, including 45,826 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 0.77 (45826 hom., cov: 30)
• Consequence: LOC730100 NR_135237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

(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 (AMR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC730100	NR_135237.1	n.753+116543A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440698.1	n.753+116543A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117236 AN: 151276 Hom.: 45818 Cov.: 30

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.775 AC: 117277 AN: 151394 Hom.: 45826 Cov.: 30 AF XY: 0.777 AC XY: 57459 AN XY: 73910

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.771

Alfa AF: 0.808 Hom.: 28131

Bravo AF: 0.772

Asia WGS AF: 0.751 AC: 2612 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	0.79
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1516174; hg19: chr2-51871341;