11-34434561-A-G

Position:

• chr11-34434561-A-G

Variant summary

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

The XR_931180.3(LOC105376622):​n.265+1444A>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 0.274 in 151,692 control chromosomes in the GnomAD database, including 6,624 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 0.27 (6624 hom., cov: 32)
• Consequence: LOC105376622 XR_931180.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

LOC105376622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376622	XR_931180.3	n.265+1444A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41533 AN: 151574 Hom.: 6623 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0438

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.274 AC: 41533 AN: 151692 Hom.: 6624 Cov.: 32 AF XY: 0.276 AC XY: 20500 AN XY: 74160

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0439

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.237

Alfa AF: 0.318 Hom.: 7837

Bravo AF: 0.246

Asia WGS AF: 0.146 AC: 509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
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: rs12807961; hg19: chr11-34456108;