rs11706236

Positions:

• chr3-55154246-A-G

Variant summary

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

The XR_007095917.1(LOC124906243):​n.159-10324T>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 0.1 in 152,182 control chromosomes in the GnomAD database, including 1,001 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 0.10 (1001 hom., cov: 32)
• Consequence: LOC124906243 XR_007095917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

LOC124906243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906243	XR_007095917.1	n.159-10324T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15272 AN: 152064 Hom.: 1000 Cov.: 32

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.100 AC: 15275 AN: 152182 Hom.: 1001 Cov.: 32 AF XY: 0.0991 AC XY: 7371 AN XY: 74392

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.0664

Gnomad4 ASJ AF: 0.0938

Gnomad4 EAS AF: 0.0700

Gnomad4 SAS AF: 0.0664

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0969

Alfa AF: 0.131 Hom.: 1200

Bravo AF: 0.0912

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11706236; hg19: chr3-55188273;