rs6550308

Positions:

• chr3-34895077-A-G

Variant summary

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

The NR_110817.1(LOC101928135):​n.207-15611T>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 0.353 in 151,914 control chromosomes in the GnomAD database, including 9,731 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 0.35 (9731 hom., cov: 32)
• Consequence: LOC101928135 NR_110817.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928135	NR_110817.1	n.207-15611T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53586 AN: 151796 Hom.: 9719 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.353 AC: 53629 AN: 151914 Hom.: 9731 Cov.: 32 AF XY: 0.353 AC XY: 26177 AN XY: 74256

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.331

Alfa AF: 0.339 Hom.: 3365

Bravo AF: 0.360

Asia WGS AF: 0.360 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
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: rs6550308; hg19: chr3-34936569;