rs12996442

chr2-37775714-T-G

Variant summary

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

The XR_001739409.2(LOC107985869):n.235-9476T>G 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 0.225 in 152,230 control chromosomes in the GnomAD database, including 4,356 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 0.22 (4356 hom., cov: 32)
• Consequence: LOC107985869 XR_001739409.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.32

Genes affected

LOC107985869 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985869	XR_001739409.2	n.235-9476T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34178 AN: 152112 Hom.: 4352 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.225 AC: 34199 AN: 152230 Hom.: 4356 Cov.: 32 AF XY: 0.230 AC XY: 17112 AN XY: 74422

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.238

Alfa AF: 0.233 Hom.: 874

Bravo AF: 0.212

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	14
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12996442; hg19: chr2-38002857;