1-91559705-A-G

Position:

• chr1-91559705-A-G

Variant summary

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

The variant allele was found at a frequency of 0.813 in 152,100 control chromosomes in the GnomAD database, including 51,101 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 0.81 (51101 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91559705A>G		intergenic_region
LOC102723436	XR_007066219.1	n.717+1686T>C		intron_variant
LOC102723436	XR_007066220.1	n.446+1686T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123516 AN: 151982 Hom.: 51078 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.813 AC: 123587 AN: 152100 Hom.: 51101 Cov.: 32 AF XY: 0.813 AC XY: 60440 AN XY: 74370

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.834

Alfa AF: 0.863 Hom.: 30447

Bravo AF: 0.814

Asia WGS AF: 0.940 AC: 3268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6687904; hg19: chr1-92025262;