rs17045031

Positions:

• chr3-66717940-G-A

Variant summary

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

The XR_940935.3(LOC105377142):​n.185+4C>T variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 152,126 control chromosomes in the GnomAD database, including 1,505 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 0.097 (1505 hom., cov: 32)
• Consequence: LOC105377142 XR_940935.3 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

Genes affected

LOC105377142 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377142	XR_940935.3	n.185+4C>T		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14740 AN: 152008 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.0970 AC: 14763 AN: 152126 Hom.: 1505 Cov.: 32 AF XY: 0.0950 AC XY: 7068 AN XY: 74378

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.0584

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0347

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.0446 Hom.: 389

Bravo AF: 0.109

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17045031; hg19: chr3-66768364;