rs1545576

chr8-2778484-A-G

Variant summary

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

The NR_168443.1(LOC105377785):n.539-26102A>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 0.0155 in 152,232 control chromosomes in the GnomAD database, including 31 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 0.015 (31 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.539-26102A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654515.1	n.532-26102A>G		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.177-26102A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000670600.1	n.539-26102A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2351 AN: 152114 Hom.: 30 Cov.: 33

Gnomad AFR AF: 0.00437

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.00930

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.0470

Gnomad FIN AF: 0.00829

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.0143

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

GnomAD4 genome AF: 0.0155 AC: 2354 AN: 152232 Hom.: 31 Cov.: 33 AF XY: 0.0155 AC XY: 1153 AN XY: 74442

Gnomad4 AFR AF: 0.00436

Gnomad4 AMR AF: 0.00929

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.0639

Gnomad4 SAS AF: 0.0470

Gnomad4 FIN AF: 0.00829

Gnomad4 NFE AF: 0.0189

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0144 Hom.: 4

Bravo AF: 0.0149

Asia WGS AF: 0.0620 AC: 215 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1545576; hg19: chr8-2636022;