rs11136949

Positions:

• chr8-5947203-G-C

Variant summary

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

The XR_941375.2(LOC105377795):​n.308-47472C>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 0.395 in 151,954 control chromosomes in the GnomAD database, including 13,024 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 0.40 (13024 hom., cov: 32)
• Consequence: LOC105377795 XR_941375.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

Genes affected

LOC105377795 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377795	XR_941375.2	n.308-47472C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60029 AN: 151836 Hom.: 13018 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.395 AC: 60054 AN: 151954 Hom.: 13024 Cov.: 32 AF XY: 0.395 AC XY: 29307 AN XY: 74274

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.398

Alfa AF: 0.435 Hom.: 1892

Bravo AF: 0.380

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
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: rs11136949; hg19: chr8-5804725;