rs7944397

chr11-34433762-A-Gchr11-34433762-A-T

Variant summary

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

The XR_931180.3(LOC105376622):n.265+645A>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 0.224 in 152,182 control chromosomes in the GnomAD database, including 5,103 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 0.22 (5103 hom., cov: 33)
• Consequence: LOC105376622 XR_931180.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

LOC105376622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376622	XR_931180.3	n.265+645A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33951 AN: 152064 Hom.: 5080 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.224 AC: 34021 AN: 152182 Hom.: 5103 Cov.: 33 AF XY: 0.217 AC XY: 16179 AN XY: 74402

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.233

Alfa AF: 0.151 Hom.: 2963

Bravo AF: 0.241

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	8.1
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7944397; hg19: chr11-34455309;