2-85538318-T-G

Position:

• chr2-85538318-T-G

Variant summary

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

The NR_038942.1(PARTICL):​n.569A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,210 control chromosomes in the GnomAD database, including 6,952 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 0.30 (6952 hom., cov: 31)
• Consequence: PARTICL NR_038942.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

Genes affected

PARTICL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARTICL	NR_038942.1	n.569A>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARTICL	ENST00000667933.2	n.466A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45123 AN: 151090 Hom.: 6941 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.299 AC: 45160 AN: 151210 Hom.: 6952 Cov.: 31 AF XY: 0.297 AC XY: 21919 AN XY: 73882

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.283

Alfa AF: 0.270 Hom.: 749

Bravo AF: 0.298

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446667; hg19: chr2-85765441;