chr2-51440601-C-A

Position:

• chr2-51440601-C-A

Variant summary

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

The NR_135237.1(LOC730100):​n.694+62428C>A 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 0.0325 in 151,840 control chromosomes in the GnomAD database, including 113 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 0.032 (113 hom., cov: 31)
• Consequence: LOC730100 NR_135237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

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 (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC730100	NR_135237.1	n.694+62428C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440698.1	n.694+62428C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0325 AC: 4927 AN: 151722 Hom.: 112 Cov.: 31

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0467

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

GnomAD4 genome AF: 0.0325 AC: 4930 AN: 151840 Hom.: 113 Cov.: 31 AF XY: 0.0327 AC XY: 2425 AN XY: 74176

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.0219

Gnomad4 ASJ AF: 0.0628

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0458

Alfa AF: 0.0278 Hom.: 52

Bravo AF: 0.0340

Asia WGS AF: 0.0770 AC: 266 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1206397; hg19: chr2-51667739;