rs7336933

chr13-41984940-G-A

Variant summary

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

The XR_941905.3(LOC105370176):n.243-10025C>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 0.166 in 152,132 control chromosomes in the GnomAD database, including 2,436 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 0.17 (2436 hom., cov: 32)
• Consequence: LOC105370176 XR_941905.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

Genes affected

LOC105370176 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370176	XR_941905.3	n.243-10025C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25183 AN: 152014 Hom.: 2433 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.166 AC: 25195 AN: 152132 Hom.: 2436 Cov.: 32 AF XY: 0.162 AC XY: 12070 AN XY: 74396

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0282

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.136

Alfa AF: 0.146 Hom.: 1599

Bravo AF: 0.166

Asia WGS AF: 0.0340 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.0090
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7336933; hg19: chr13-42559076;