1-5335808-A-G

Variant names:

• chr1-5335808-A-G
• rs729206

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.463 in 152,030 control chromosomes in the GnomAD database, including 16,690 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 0.46 (16690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70395 AN: 151912 Hom.: 16669 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.463 AC: 70454 AN: 152030 Hom.: 16690 Cov.: 32 AF XY: 0.471 AC XY: 34978 AN XY: 74292

African (AFR) AF: 0.499 AC: 20710 AN: 41474

American (AMR) AF: 0.461 AC: 7048 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1705 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3628 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4818

European-Finnish (FIN) AF: 0.535 AC: 5640 AN: 10544

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27956 AN: 67968

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.326 Hom.: 853

Bravo AF: 0.457

Asia WGS AF: 0.608 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.60
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs729206; hg19: chr1-5395868;