rs3181225

Positions:

• chr5-159313615-G-A

Variant summary

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

The XR_941138.3(LOC105377683):​n.401-1603G>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 0.15 in 152,210 control chromosomes in the GnomAD database, including 1,951 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 0.15 (1951 hom., cov: 32)
• Consequence: LOC105377683 XR_941138.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

Genes affected

LOC105377683 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377683	XR_941138.3	n.401-1603G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000521472.6	n.289+2201G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22860 AN: 152092 Hom.: 1947 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.150 AC: 22872 AN: 152210 Hom.: 1951 Cov.: 32 AF XY: 0.152 AC XY: 11340 AN XY: 74422

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.165

Alfa AF: 0.173 Hom.: 2373

Bravo AF: 0.140

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181225; hg19: chr5-158740623;