rs10767873

chr11-30747131-C-T

Variant summary

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

The XR_007062640.1(LOC101928338):n.249+5545C>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 0.357 in 151,894 control chromosomes in the GnomAD database, including 11,420 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 0.36 (11420 hom., cov: 32)
• Consequence: LOC101928338 XR_007062640.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

LOC101928338 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928338	XR_007062640.1	n.249+5545C>T		intron_variant, non_coding_transcript_variant
LOC101928338	XR_242862.5	n.249+5545C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54212 AN: 151776 Hom.: 11424 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.357 AC: 54211 AN: 151894 Hom.: 11420 Cov.: 32 AF XY: 0.358 AC XY: 26551 AN XY: 74228

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.383

Alfa AF: 0.439 Hom.: 13998

Bravo AF: 0.344

Asia WGS AF: 0.322 AC: 1119 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.6
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10767873; hg19: chr11-30768678;