rs1328950

chr13-31442143-A-Gchr13-31442143-A-T

Variant summary

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

The XR_941830.1(LOC105370150):n.233+963A>G 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 0.141 in 152,148 control chromosomes in the GnomAD database, including 1,601 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 0.14 (1601 hom., cov: 32)
• Consequence: LOC105370150 XR_941830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

Genes affected

LOC105370150 (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 = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370150	XR_941830.1	n.233+963A>G		intron_variant, non_coding_transcript_variant
LOC105370150	XR_001749806.1	n.359+963A>G		intron_variant, non_coding_transcript_variant
LOC105370150	XR_941829.1	n.231+963A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21505 AN: 152028 Hom.: 1600 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.141 AC: 21520 AN: 152148 Hom.: 1601 Cov.: 32 AF XY: 0.145 AC XY: 10801 AN XY: 74386

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0578 Hom.: 60

Bravo AF: 0.137

Asia WGS AF: 0.275 AC: 955 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	4.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328950; hg19: chr13-32016280;