rs12989701

chr2-127130409-C-A

Variant summary

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

The XR_923311.4(LOC105373605):n.846-2829C>A 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 0.127 in 152,242 control chromosomes in the GnomAD database, including 1,337 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 0.13 (1337 hom., cov: 32)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4	n.846-2829C>A		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.449-2829C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19381 AN: 152124 Hom.: 1334 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.127 AC: 19398 AN: 152242 Hom.: 1337 Cov.: 32 AF XY: 0.124 AC XY: 9250 AN XY: 74450

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.0732

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.123

Alfa AF: 0.141 Hom.: 2247

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12989701; hg19: chr2-127887985;