rs6868898

Positions:

• chr5-159337412-T-C

Variant summary

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

The NR_037889.1(LOC285626):​n.745+4409T>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 0.311 in 152,110 control chromosomes in the GnomAD database, including 7,822 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 0.31 (7822 hom., cov: 33)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285626	NR_037889.1	n.745+4409T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515337.1	n.745+4409T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.324+4409T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47240 AN: 151990 Hom.: 7810 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.311 AC: 47294 AN: 152110 Hom.: 7822 Cov.: 33 AF XY: 0.318 AC XY: 23675 AN XY: 74344

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.282

Alfa AF: 0.316 Hom.: 7048

Bravo AF: 0.304

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6868898; hg19: chr5-158764420;