rs181781

chr5-132059422-G-A

Variant summary

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

The XR_001742531.2(LOC105379174):n.211+2049C>T 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 0.0934 in 152,122 control chromosomes in the GnomAD database, including 959 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 0.093 (959 hom., cov: 32)
• Consequence: LOC105379174 XR_001742531.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

LOC105379174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379174	XR_001742531.2	n.211+2049C>T		intron_variant, non_coding_transcript_variant
LOC105379174	XR_948784.3	n.398+2049C>T		intron_variant, non_coding_transcript_variant
LOC105379174	XR_948785.3	n.228+2049C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14209 AN: 152004 Hom.: 962 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0944

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

GnomAD4 genome AF: 0.0934 AC: 14207 AN: 152122 Hom.: 959 Cov.: 32 AF XY: 0.0975 AC XY: 7254 AN XY: 74368

Gnomad4 AFR AF: 0.0270

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0958

Alfa AF: 0.0991 Hom.: 839

Bravo AF: 0.0836

Asia WGS AF: 0.191 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181781; hg19: chr5-131395115;