rs3858772

chr13-97674394-A-T

Variant summary

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

The XR_007063845.1(LOC105370324):n.2614+3397T>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 0.122 in 152,196 control chromosomes in the GnomAD database, including 1,260 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 0.12 (1260 hom., cov: 31)
• Consequence: LOC105370324 XR_007063845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

Genes affected

LOC105370324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370324	XR_007063845.1	n.2614+3397T>A		intron_variant, non_coding_transcript_variant
LOC105370324	XR_931663.3	n.2670+3397T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18482 AN: 152078 Hom.: 1263 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.122 AC: 18492 AN: 152196 Hom.: 1260 Cov.: 31 AF XY: 0.126 AC XY: 9354 AN XY: 74422

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0923

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0963

Gnomad4 OTH AF: 0.131

Alfa AF: 0.107 Hom.: 106

Bravo AF: 0.122

Asia WGS AF: 0.238 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.1
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3858772; hg19: chr13-98326648;