rs7533689

Variant names:

• chr1-212415353-G-A
• rs7533689

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 0.258 in 152,148 control chromosomes in the GnomAD database, including 6,821 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 0.26 (6821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.258 AC: 39161 AN: 152030 Hom.: 6801 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.258 AC: 39218 AN: 152148 Hom.: 6821 Cov.: 32 AF XY: 0.252 AC XY: 18726 AN XY: 74408

African (AFR) AF: 0.495 AC: 20530 AN: 41456

American (AMR) AF: 0.165 AC: 2520 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5188

South Asian (SAS) AF: 0.205 AC: 990 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1596 AN: 10598

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12194 AN: 68002

Other (OTH) AF: 0.245 AC: 519 AN: 2116

Alfa AF: 0.213 Hom.: 687

Bravo AF: 0.266

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.30
PromoterAI		-0.021	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7533689; hg19: chr1-212588695;