8-124729925-A-G

Variant names:

• chr8-124729925-A-G
• rs891541
• XR_001745686.3:n.1387A>G

Variant summary

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

The XR_928609.4(LOC105375741):​n.1387A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,084 control chromosomes in the GnomAD database, including 35,949 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 0.68 (35949 hom., cov: 32)
• Consequence: LOC105375741 XR_928609.4 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

Genes affected

LOC105375741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375741	XR_001745686.3	n.1387A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105375741	XR_001745687.3	n.1387A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 3
LOC105375741	XR_001745688.3	n.1387A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103573 AN: 151966 Hom.: 35913 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.682 AC: 103665 AN: 152084 Hom.: 35949 Cov.: 32 AF XY: 0.681 AC XY: 50655 AN XY: 74344

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.712

Alfa AF: 0.731 Hom.: 38653

Bravo AF: 0.683

Asia WGS AF: 0.613 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs891541; hg19: chr8-125742166;