rs7520850

Variant names:

• chr1-46417996-G-A
• rs7520850

Your query was ambiguous. Multiple possible variants found:

• chr1-46417996-G-A
• chr1-46417996-G-C

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 0.105 in 152,226 control chromosomes in the GnomAD database, including 922 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 0.10 (922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.105 AC: 15904 AN: 152108 Hom.: 920 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.105 AC: 15938 AN: 152226 Hom.: 922 Cov.: 33 AF XY: 0.103 AC XY: 7645 AN XY: 74426

African (AFR) AF: 0.132 AC: 5470 AN: 41528

American (AMR) AF: 0.0744 AC: 1138 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.154 AC: 745 AN: 4830

European-Finnish (FIN) AF: 0.0518 AC: 549 AN: 10606

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7190 AN: 68000

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.0920 Hom.: 409

Bravo AF: 0.104

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs7520850; hg19: chr1-46883668;