rs1454974

Positions:

• chr8-2804227-C-G

Variant summary

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

The NR_168443.1(LOC105377785):​n.539-359C>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 0.0124 in 151,962 control chromosomes in the GnomAD database, including 23 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 0.012 (23 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.947

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.539-359C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654515.1	n.532-359C>G		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.177-359C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000662575.1	n.82-359C>G		intron_variant, non_coding_transcript_variant
	ENST00000670600.1	n.539-359C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1883 AN: 151844 Hom.: 21 Cov.: 33

Gnomad AFR AF: 0.00378

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00788

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.00570

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0124 AC: 1889 AN: 151962 Hom.: 23 Cov.: 33 AF XY: 0.0127 AC XY: 941 AN XY: 74258

Gnomad4 AFR AF: 0.00376

Gnomad4 AMR AF: 0.00787

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.0402

Gnomad4 FIN AF: 0.00570

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0104 Hom.: 2

Bravo AF: 0.0122

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454974; hg19: chr8-2661745;