rs12541063

chr8-134857733-A-Gchr8-134857733-A-T

Variant summary

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

The NR_125427.1(LOC101927845):n.1696+6103A>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 0.777 in 152,144 control chromosomes in the GnomAD database, including 46,084 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 0.78 (46084 hom., cov: 31)
• Consequence: LOC101927845 NR_125427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927845	NR_125427.1	n.1696+6103A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000505083.1	n.1696+6103A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118188 AN: 152026 Hom.: 46051 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.777 AC: 118279 AN: 152144 Hom.: 46084 Cov.: 31 AF XY: 0.774 AC XY: 57533 AN XY: 74370

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.775

Alfa AF: 0.775 Hom.: 7308

Bravo AF: 0.780

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.3
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: rs12541063; hg19: chr8-135869976;