rs1024008

chr3-72629872-A-Gchr3-72629872-A-T

Variant summary

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

The XR_940962.3(LOC105377161):n.851+8574T>C 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 0.518 in 152,134 control chromosomes in the GnomAD database, including 20,675 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 0.52 (20675 hom., cov: 33)
• Consequence: LOC105377161 XR_940962.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846

Genes affected

LOC105377161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377161	XR_940962.3	n.851+8574T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78808 AN: 152016 Hom.: 20649 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.518 AC: 78879 AN: 152134 Hom.: 20675 Cov.: 33 AF XY: 0.523 AC XY: 38889 AN XY: 74380

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.527

Alfa AF: 0.419 Hom.: 1795

Bravo AF: 0.523

Asia WGS AF: 0.646 AC: 2246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.97
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024008; hg19: chr3-72679023;