2-81592427-T-C

Variant summary

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

The XR_007088668.1(LOC102724542):n.667+12818T>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 0.245 in 152,040 control chromosomes in the GnomAD database, including 5,111 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 0.24 (5111 hom., cov: 32)
• Consequence: LOC102724542 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724542	XR_007088668.1	n.667+12818T>C		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.575+12818T>C		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.497+43680T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37169 AN: 151922 Hom.: 5104 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.245 AC: 37194 AN: 152040 Hom.: 5111 Cov.: 32 AF XY: 0.240 AC XY: 17825 AN XY: 74286

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.229

Alfa AF: 0.301 Hom.: 7702

Bravo AF: 0.235

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.3
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7570909; hg19: chr2-81819551;