3-45315474-G-A

Position:

• chr3-45315474-G-A

Variant summary

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

The XR_001740679.1(LOC105377061):​n.980+5323G>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 0.0565 in 152,238 control chromosomes in the GnomAD database, including 696 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 0.057 (696 hom., cov: 32)
• Consequence: LOC105377061 XR_001740679.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

LOC105377061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377061	XR_001740679.1	n.980+5323G>A		intron_variant, non_coding_transcript_variant
LOC105377061	XR_001740678.1	n.980+5323G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 8550 AN: 152120 Hom.: 689 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.00318

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00294

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0565 AC: 8602 AN: 152238 Hom.: 696 Cov.: 32 AF XY: 0.0562 AC XY: 4183 AN XY: 74450

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.00318

Gnomad4 EAS AF: 0.0241

Gnomad4 SAS AF: 0.0784

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00294

Gnomad4 OTH AF: 0.0425

Alfa AF: 0.0350 Hom.: 60

Bravo AF: 0.0627

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9846284; hg19: chr3-45356966;