rs1431659

Positions:

• chr8-72526835-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 0.738 in 151,994 control chromosomes in the GnomAD database, including 41,518 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 0.74 (41518 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72526835A>G		intergenic_region
LOC105375897	XR_929042.3	n.797+4715T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112127 AN: 151876 Hom.: 41476 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.738 AC: 112222 AN: 151994 Hom.: 41518 Cov.: 31 AF XY: 0.740 AC XY: 54917 AN XY: 74262

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.727

Alfa AF: 0.744 Hom.: 7122

Bravo AF: 0.744

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1431659; hg19: chr8-73439070;