2-15786044-T-C

Position:

• chr2-15786044-T-C

Variant summary

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

The XR_007086225.1(LOC124905976):​n.1147T>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 0.773 in 152,122 control chromosomes in the GnomAD database, including 46,544 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 (46544 hom., cov: 32)
• Consequence: LOC124905976 XR_007086225.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC124905976 (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 (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905976	XR_007086225.1	n.1147T>C		non_coding_transcript_exon_variant	3/3
		n.15786044T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117478 AN: 152004 Hom.: 46480 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.773 AC: 117601 AN: 152122 Hom.: 46544 Cov.: 32 AF XY: 0.774 AC XY: 57566 AN XY: 74328

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.763

Alfa AF: 0.702 Hom.: 68614

Bravo AF: 0.786

Asia WGS AF: 0.764 AC: 2660 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	0.16
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2544527; hg19: chr2-15926168;