rs4972990

Positions:

• chr2-231414300-T-C

Variant summary

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

The XR_007088118.1(LOC124907997):​n.955T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,096 control chromosomes in the GnomAD database, including 10,667 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 0.37 (10667 hom., cov: 32)
• Consequence: LOC124907997 XR_007088118.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

LOC124907997 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907997	XR_007088118.1	n.955T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56626 AN: 151978 Hom.: 10668 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.372 AC: 56647 AN: 152096 Hom.: 10667 Cov.: 32 AF XY: 0.372 AC XY: 27692 AN XY: 74378

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.379

Alfa AF: 0.379 Hom.: 2191

Bravo AF: 0.367

Asia WGS AF: 0.403 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4972990; hg19: chr2-232279011;