2-193119895-A-G

Position:

• chr2-193119895-A-G

Variant summary

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

The XR_001739832.2(LOC107985969):​n.233+40425T>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 0.059 in 152,138 control chromosomes in the GnomAD database, including 412 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 0.059 (412 hom., cov: 32)
• Consequence: LOC107985969 XR_001739832.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

LOC107985969 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985969	XR_001739832.2	n.233+40425T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8979 AN: 152020 Hom.: 411 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0590 AC: 8974 AN: 152138 Hom.: 412 Cov.: 32 AF XY: 0.0594 AC XY: 4419 AN XY: 74374

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0239

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.0550

Alfa AF: 0.0690 Hom.: 727

Bravo AF: 0.0633

Asia WGS AF: 0.0150 AC: 53 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17662626; hg19: chr2-193984621;