rs17027938

chr3-86733823-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_941027.4(LOC101927518):n.269-3355A>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 0.118 in 152,198 control chromosomes in the GnomAD database, including 2,173 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 0.12 (2173 hom., cov: 33)
• Consequence: LOC101927518 XR_941027.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

Genes affected

LOC101927518 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927518	XR_941027.4	n.269-3355A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17947 AN: 152080 Hom.: 2148 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.118 AC: 18015 AN: 152198 Hom.: 2173 Cov.: 33 AF XY: 0.123 AC XY: 9129 AN XY: 74410

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.0912

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0458 Hom.: 1377

Bravo AF: 0.140

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	16
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17027938; hg19: chr3-86782973;