2-56627439-G-C

Variant summary

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

The XR_001739478.1(LOC101927213):n.289-21633G>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 0.429 in 151,828 control chromosomes in the GnomAD database, including 15,458 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 0.43 (15458 hom., cov: 31)
• Consequence: LOC101927213 XR_001739478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

LOC101927213 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927213	XR_001739478.1	n.289-21633G>C		intron_variant, non_coding_transcript_variant
LOC101927213	XR_001739479.1	n.289-16373G>C		intron_variant, non_coding_transcript_variant
LOC101927213	XR_001739480.1	n.330-16373G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65143 AN: 151710 Hom.: 15454 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.429 AC: 65141 AN: 151828 Hom.: 15458 Cov.: 31 AF XY: 0.436 AC XY: 32326 AN XY: 74164

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.454

Alfa AF: 0.341 Hom.: 999

Bravo AF: 0.405

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.17
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17268959; hg19: chr2-56854574;