rs7118388

Positions:

• chr11-34432600-A-G
• chr11-34432600-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.159+153A>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 0.514 in 151,864 control chromosomes in the GnomAD database, including 20,798 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 0.51 (20798 hom., cov: 31)
• Consequence: LOC105376622 XR_931180.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

LOC105376622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376622	XR_931180.3	n.159+153A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77965 AN: 151746 Hom.: 20761 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.514 AC: 78041 AN: 151864 Hom.: 20798 Cov.: 31 AF XY: 0.510 AC XY: 37865 AN XY: 74222

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.478

Alfa AF: 0.488 Hom.: 39276

Bravo AF: 0.506

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7118388; hg19: chr11-34454147;