rs3097167

Positions:

• chr5-116789382-G-A
• chr5-116789382-G-C

Variant summary

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

The XR_948689.3(LOC105379133):​n.149-17509G>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 0.849 in 152,186 control chromosomes in the GnomAD database, including 55,147 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 0.85 (55147 hom., cov: 32)
• Consequence: LOC105379133 XR_948689.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

Genes affected

LOC105379133 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379133	XR_948689.3	n.149-17509G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129107 AN: 152068 Hom.: 55111 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.849 AC: 129197 AN: 152186 Hom.: 55147 Cov.: 32 AF XY: 0.843 AC XY: 62746 AN XY: 74396

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.841

Alfa AF: 0.833 Hom.: 71460

Bravo AF: 0.857

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3097167; hg19: chr5-116125078;