rs727248

Positions:

• chr2-51353418-A-G

Variant summary

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

The ENST00000440698.1(ENSG00000231918):​n.616-24677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 152,234 control chromosomes in the GnomAD database, including 365 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 0.049 (365 hom., cov: 32)
• Consequence: ENSG00000231918 ENST00000440698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

Genes affected

ENSG00000231918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRXN1-DT	NR_135237.1	n.616-24677A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231918	ENST00000440698.1	n.616-24677A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7396 AN: 152116 Hom.: 361 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0487 AC: 7409 AN: 152234 Hom.: 365 Cov.: 32 AF XY: 0.0528 AC XY: 3934 AN XY: 74452

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0250

Gnomad4 NFE AF: 0.0274

Gnomad4 OTH AF: 0.0671

Alfa AF: 0.0369 Hom.: 36

Bravo AF: 0.0581

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.30
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727248; hg19: chr2-51580556;