rs1381801

chr3-117522048-A-T

Variant summary

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

The XR_924361.3(LOC105374056):n.30063+7548A>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 0.487 in 152,010 control chromosomes in the GnomAD database, including 19,434 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 0.49 (19434 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374056	XR_924361.3	n.30063+7548A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74054 AN: 151892 Hom.: 19435 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.487 AC: 74061 AN: 152010 Hom.: 19434 Cov.: 32 AF XY: 0.481 AC XY: 35737 AN XY: 74306

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.506

Alfa AF: 0.534 Hom.: 2792

Bravo AF: 0.476

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381801; hg19: chr3-117240895;