rs2912600

Positions:

• chr15-26475396-A-G

Variant summary

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

The ENST00000660088.1(ENSG00000287280):​n.120+2325T>C 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 0.277 in 152,126 control chromosomes in the GnomAD database, including 9,402 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 0.28 (9402 hom., cov: 32)
• Consequence: ENST00000660088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02248	XR_001751453.2	n.2695-14116A>G		intron_variant, non_coding_transcript_variant
LOC105370740	XR_007064792.1	n.418+2325T>C		intron_variant, non_coding_transcript_variant
LOC105370740	XR_007064791.1	n.418+2325T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660088.1	n.120+2325T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 42017 AN: 152008 Hom.: 9374 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.277 AC: 42086 AN: 152126 Hom.: 9402 Cov.: 32 AF XY: 0.273 AC XY: 20271 AN XY: 74384

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.274

Alfa AF: 0.161 Hom.: 4002

Bravo AF: 0.300

Asia WGS AF: 0.204 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2912600; hg19: chr15-26720543;