1-154628681-A-G

Position:

• chr1-154628681-A-G

Variant summary

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

The XR_007066635.1(LOC124904427):​n.112+614A>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 0.349 in 152,186 control chromosomes in the GnomAD database, including 11,181 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 0.35 (11181 hom., cov: 33)
• Consequence: LOC124904427 XR_007066635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712

Genes affected

LOC124904427 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904427	XR_007066635.1	n.112+614A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53138 AN: 152068 Hom.: 11181 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.349 AC: 53138 AN: 152186 Hom.: 11181 Cov.: 33 AF XY: 0.353 AC XY: 26230 AN XY: 74380

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.361

Alfa AF: 0.411 Hom.: 5415

Bravo AF: 0.344

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884618; hg19: chr1-154601157;