1-35208710-A-G

Position:

• chr1-35208710-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 0.249 in 151,830 control chromosomes in the GnomAD database, including 7,912 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 0.25 (7912 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35208710A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37702 AN: 151712 Hom.: 7874 Cov.: 29

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.249 AC: 37805 AN: 151830 Hom.: 7912 Cov.: 29 AF XY: 0.250 AC XY: 18585 AN XY: 74196

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.0894

Gnomad4 NFE AF: 0.0835

Gnomad4 OTH AF: 0.226

Alfa AF: 0.115 Hom.: 3641

Bravo AF: 0.279

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543044; hg19: chr1-35674311;