rs6556412

Positions:

• chr5-159360377-G-A

Variant summary

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

The NR_037889.1(LOC285626):​n.954-1831G>A 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 0.336 in 152,092 control chromosomes in the GnomAD database, including 8,686 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 0.34 (8686 hom., cov: 32)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.954-1831G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000515337.1	n.954-1831G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000635333.1	n.282+6256G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000641150.1	n.532+6256G>A		intron_variant, non_coding_transcript_variant
	ENST00000648969.1	n.53+6256G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51120 AN: 151972 Hom.: 8680 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.336 AC: 51153 AN: 152092 Hom.: 8686 Cov.: 32 AF XY: 0.336 AC XY: 24980 AN XY: 74328

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.352

Alfa AF: 0.335 Hom.: 13661

Bravo AF: 0.338

Asia WGS AF: 0.442 AC: 1539 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	0.23
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6556412; hg19: chr5-158787385;