rs7941248

chr11-33904428-T-C

Variant summary

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

The XR_931176.3(LOC105376621):n.91-2181T>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 0.705 in 151,858 control chromosomes in the GnomAD database, including 38,293 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 0.71 (38293 hom., cov: 29)
• Consequence: LOC105376621 XR_931176.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

LOC105376621 (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 = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376621	XR_931176.3	n.91-2181T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107036 AN: 151742 Hom.: 38259 Cov.: 29

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.705 AC: 107117 AN: 151858 Hom.: 38293 Cov.: 29 AF XY: 0.701 AC XY: 52006 AN XY: 74186

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.666

Alfa AF: 0.695 Hom.: 75227

Bravo AF: 0.698

Asia WGS AF: 0.524 AC: 1823 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	1.0
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: rs7941248; hg19: chr11-33925975;