3-86156073-T-C

Position:

• chr3-86156073-T-C

Variant summary

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

The XR_941024.3(LOC102723364):​n.683-19228A>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 0.538 in 151,932 control chromosomes in the GnomAD database, including 22,338 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 0.54 (22338 hom., cov: 32)
• Consequence: LOC102723364 XR_941024.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

LOC102723364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723364	XR_941024.3	n.683-19228A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81723 AN: 151814 Hom.: 22332 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.538 AC: 81757 AN: 151932 Hom.: 22338 Cov.: 32 AF XY: 0.539 AC XY: 39988 AN XY: 74242

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.529

Alfa AF: 0.562 Hom.: 15881

Bravo AF: 0.527

Asia WGS AF: 0.503 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12636212; hg19: chr3-86205223;